Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 20:23:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/07_2023/7bw4_30226.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/07_2023/7bw4_30226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/07_2023/7bw4_30226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/07_2023/7bw4_30226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/07_2023/7bw4_30226.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/07_2023/7bw4_30226.pdb" } resolution = 3.7 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 63 5.16 5 C 5503 2.51 5 N 1430 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ASP 804": "OD1" <-> "OD2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A ASP 824": "OD1" <-> "OD2" Residue "A ASP 825": "OD1" <-> "OD2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8605 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6541 Classifications: {'peptide': 811} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 783} Chain breaks: 2 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "D" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 676 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1681 SG CYS A 301 37.606 64.202 36.311 1.00 60.22 S ATOM 1722 SG CYS A 306 37.746 61.966 32.323 1.00 54.47 S ATOM 1754 SG CYS A 310 40.444 62.538 35.190 1.00 51.56 S ATOM 3162 SG CYS A 487 18.959 60.096 44.561 1.00 74.40 S ATOM 4415 SG CYS A 645 18.857 59.240 41.138 1.00 73.86 S ATOM 4421 SG CYS A 646 21.336 61.568 42.144 1.00 71.79 S Time building chain proxies: 4.29, per 1000 atoms: 0.50 Number of scatterers: 8605 At special positions: 0 Unit cell: (80.8, 95.2, 124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 63 16.00 O 1607 8.00 N 1430 7.00 C 5503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 51.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 4.058A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.611A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.590A pdb=" N TYR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.628A pdb=" N CYS A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.781A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.615A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.200A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.710A pdb=" N ASN A 300 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.938A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 458 Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.735A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.649A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 641 removed outlier: 3.728A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 684 through 709 removed outlier: 4.208A pdb=" N ALA A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.952A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.571A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.648A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 866 removed outlier: 4.046A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.166A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.648A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.608A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.601A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.020A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.563A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.649A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.775A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.576A pdb=" N ASN D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 4.178A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 44 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 5.836A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.320A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.567A pdb=" N VAL B 131 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.427A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA9, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.120A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 188 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 130 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 186 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU D 155 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 142 through 143 396 hydrogen bonds defined for protein. 1131 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: 2.60 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2411 1.33 - 1.45: 1541 1.45 - 1.57: 4746 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 8794 Sorted by residual: bond pdb=" N LEU A 401 " pdb=" CA LEU A 401 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.37e-02 5.33e+03 8.89e+00 bond pdb=" N THR A 248 " pdb=" CA THR A 248 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.37e-02 5.33e+03 8.86e+00 bond pdb=" N ARG A 249 " pdb=" CA ARG A 249 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N VAL A 166 " pdb=" CA VAL A 166 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N VAL A 174 " pdb=" CA VAL A 174 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 ... (remaining 8789 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 209 106.57 - 113.42: 4782 113.42 - 120.27: 3305 120.27 - 127.13: 3563 127.13 - 133.98: 79 Bond angle restraints: 11938 Sorted by residual: angle pdb=" C THR A 248 " pdb=" CA THR A 248 " pdb=" CB THR A 248 " ideal model delta sigma weight residual 109.55 116.90 -7.35 1.68e+00 3.54e-01 1.91e+01 angle pdb=" C VAL A 166 " pdb=" CA VAL A 166 " pdb=" CB VAL A 166 " ideal model delta sigma weight residual 111.29 104.38 6.91 1.64e+00 3.72e-01 1.78e+01 angle pdb=" N VAL A 166 " pdb=" CA VAL A 166 " pdb=" C VAL A 166 " ideal model delta sigma weight residual 109.34 117.99 -8.65 2.08e+00 2.31e-01 1.73e+01 angle pdb=" N ASN A 447 " pdb=" CA ASN A 447 " pdb=" C ASN A 447 " ideal model delta sigma weight residual 111.71 106.96 4.75 1.15e+00 7.56e-01 1.71e+01 angle pdb=" N LEU A 247 " pdb=" CA LEU A 247 " pdb=" C LEU A 247 " ideal model delta sigma weight residual 111.82 107.38 4.44 1.16e+00 7.43e-01 1.47e+01 ... (remaining 11933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4637 17.99 - 35.98: 495 35.98 - 53.97: 78 53.97 - 71.95: 12 71.95 - 89.94: 8 Dihedral angle restraints: 5230 sinusoidal: 2035 harmonic: 3195 Sorted by residual: dihedral pdb=" CA ASP D 161 " pdb=" C ASP D 161 " pdb=" N ALA D 162 " pdb=" CA ALA D 162 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA THR A 462 " pdb=" C THR A 462 " pdb=" N MET A 463 " pdb=" CA MET A 463 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA TRP A 617 " pdb=" C TRP A 617 " pdb=" N ASP A 618 " pdb=" CA ASP A 618 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 988 0.055 - 0.111: 295 0.111 - 0.166: 53 0.166 - 0.221: 11 0.221 - 0.276: 3 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA LEU A 251 " pdb=" N LEU A 251 " pdb=" C LEU A 251 " pdb=" CB LEU A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA THR A 248 " pdb=" N THR A 248 " pdb=" C THR A 248 " pdb=" CB THR A 248 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA SER B 177 " pdb=" N SER B 177 " pdb=" C SER B 177 " pdb=" CB SER B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1347 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 686 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C THR A 686 " 0.063 2.00e-02 2.50e+03 pdb=" O THR A 686 " -0.024 2.00e-02 2.50e+03 pdb=" N THR A 687 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 572 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C HIS A 572 " 0.057 2.00e-02 2.50e+03 pdb=" O HIS A 572 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 573 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 570 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C GLN A 570 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN A 570 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 571 " -0.019 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 148 2.64 - 3.21: 8024 3.21 - 3.77: 13095 3.77 - 4.34: 17510 4.34 - 4.90: 28137 Nonbonded interactions: 66914 Sorted by model distance: nonbonded pdb=" O ASN A 168 " pdb=" ND2 ASN A 168 " model vdw 2.078 2.520 nonbonded pdb=" N LYS D 127 " pdb=" O ALA D 188 " model vdw 2.159 2.520 nonbonded pdb=" OG1 THR A 120 " pdb=" O TYR A 122 " model vdw 2.180 2.440 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 144 " model vdw 2.185 2.440 nonbonded pdb=" O VAL A 174 " pdb=" N ASN A 177 " model vdw 2.193 2.520 ... (remaining 66909 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: 1.190 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: 4.090 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.560 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.004 0.041 8794 Z= 0.245 Angle : 0.655 8.651 11938 Z= 0.421 Chirality : 0.055 0.276 1350 Planarity : 0.004 0.042 1517 Dihedral : 15.164 89.943 3164 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.34 % Favored : 95.47 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.22), residues: 1060 helix: -0.74 (0.21), residues: 493 sheet: -1.63 (0.55), residues: 76 loop : -2.66 (0.22), residues: 491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 268 average time/residue: 0.2555 time to fit residues: 88.9836 Evaluate side-chains 188 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0881 time to fit residues: 2.4329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.0770 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.0270 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.0970 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 0.0670 chunk 96 optimal weight: 0.0370 overall best weight: 0.0610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 439 HIS A 447 ASN A 572 HIS A 650 HIS ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A 789 GLN A 928 HIS B 104 ASN B 109 ASN D 104 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8794 Z= 0.166 Angle : 0.617 8.854 11938 Z= 0.327 Chirality : 0.044 0.209 1350 Planarity : 0.004 0.049 1517 Dihedral : 5.092 19.387 1172 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.60 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1060 helix: 0.11 (0.23), residues: 503 sheet: -1.74 (0.56), residues: 66 loop : -2.03 (0.24), residues: 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 211 average time/residue: 0.2177 time to fit residues: 62.6522 Evaluate side-chains 185 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1593 time to fit residues: 2.8615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN A 703 ASN B 118 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8794 Z= 0.235 Angle : 0.618 8.177 11938 Z= 0.334 Chirality : 0.044 0.194 1350 Planarity : 0.004 0.044 1517 Dihedral : 4.969 21.207 1172 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.09 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.24), residues: 1060 helix: 0.31 (0.23), residues: 509 sheet: -0.95 (0.58), residues: 74 loop : -2.10 (0.24), residues: 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 195 average time/residue: 0.2183 time to fit residues: 58.0260 Evaluate side-chains 183 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1031 time to fit residues: 4.2788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8794 Z= 0.249 Angle : 0.619 8.007 11938 Z= 0.335 Chirality : 0.045 0.171 1350 Planarity : 0.004 0.043 1517 Dihedral : 4.929 22.685 1172 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.28 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1060 helix: 0.31 (0.23), residues: 509 sheet: -1.03 (0.54), residues: 84 loop : -2.02 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 188 average time/residue: 0.2512 time to fit residues: 63.7095 Evaluate side-chains 173 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0897 time to fit residues: 3.9910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 HIS A 599 HIS ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 8794 Z= 0.313 Angle : 0.674 7.978 11938 Z= 0.365 Chirality : 0.046 0.236 1350 Planarity : 0.004 0.041 1517 Dihedral : 5.113 24.136 1172 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.87 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1060 helix: 0.23 (0.23), residues: 499 sheet: -1.55 (0.50), residues: 84 loop : -1.92 (0.25), residues: 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 170 average time/residue: 0.2405 time to fit residues: 55.6862 Evaluate side-chains 159 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0901 time to fit residues: 2.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8794 Z= 0.209 Angle : 0.608 7.939 11938 Z= 0.327 Chirality : 0.044 0.173 1350 Planarity : 0.004 0.045 1517 Dihedral : 4.929 23.217 1172 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1060 helix: 0.34 (0.23), residues: 503 sheet: -1.49 (0.51), residues: 84 loop : -1.77 (0.25), residues: 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 176 average time/residue: 0.2427 time to fit residues: 57.5983 Evaluate side-chains 167 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0836 time to fit residues: 2.7445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 8794 Z= 0.292 Angle : 0.661 9.622 11938 Z= 0.354 Chirality : 0.046 0.182 1350 Planarity : 0.004 0.060 1517 Dihedral : 5.070 23.962 1172 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.23 % Favored : 93.68 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.25), residues: 1060 helix: 0.28 (0.23), residues: 499 sheet: -1.36 (0.49), residues: 94 loop : -1.81 (0.26), residues: 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 0.986 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.2328 time to fit residues: 54.1922 Evaluate side-chains 162 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0834 time to fit residues: 2.6368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A 822 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8794 Z= 0.215 Angle : 0.635 9.809 11938 Z= 0.336 Chirality : 0.045 0.179 1350 Planarity : 0.004 0.057 1517 Dihedral : 4.972 26.330 1172 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.09 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1060 helix: 0.33 (0.23), residues: 499 sheet: -1.70 (0.54), residues: 74 loop : -1.78 (0.25), residues: 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 169 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 171 average time/residue: 0.2279 time to fit residues: 52.3142 Evaluate side-chains 161 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0882 time to fit residues: 1.7370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 8794 Z= 0.349 Angle : 0.727 9.092 11938 Z= 0.388 Chirality : 0.048 0.229 1350 Planarity : 0.005 0.057 1517 Dihedral : 5.269 24.469 1172 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.55 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1060 helix: 0.12 (0.23), residues: 498 sheet: -1.47 (0.53), residues: 84 loop : -1.95 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 0.2295 time to fit residues: 53.5340 Evaluate side-chains 164 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0840 time to fit residues: 2.3782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 0.0670 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8794 Z= 0.182 Angle : 0.658 9.464 11938 Z= 0.345 Chirality : 0.045 0.217 1350 Planarity : 0.004 0.056 1517 Dihedral : 4.914 22.465 1172 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.75 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1060 helix: 0.25 (0.23), residues: 502 sheet: -1.72 (0.53), residues: 80 loop : -1.73 (0.26), residues: 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 183 average time/residue: 0.2241 time to fit residues: 56.3995 Evaluate side-chains 168 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1110 time to fit residues: 1.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.138829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112503 restraints weight = 17126.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115830 restraints weight = 9725.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.118018 restraints weight = 6665.422| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8794 Z= 0.187 Angle : 0.665 9.466 11938 Z= 0.349 Chirality : 0.046 0.264 1350 Planarity : 0.004 0.055 1517 Dihedral : 4.824 22.808 1172 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1060 helix: 0.33 (0.23), residues: 496 sheet: -1.43 (0.56), residues: 78 loop : -1.61 (0.26), residues: 486 =============================================================================== Job complete usr+sys time: 1881.68 seconds wall clock time: 35 minutes 0.99 seconds (2100.99 seconds total)