Starting phenix.real_space_refine on Wed Aug 7 03:18:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/08_2024/8wa5_37391.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/08_2024/8wa5_37391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/08_2024/8wa5_37391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/08_2024/8wa5_37391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/08_2024/8wa5_37391.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/08_2024/8wa5_37391.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9918 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 6368 2.51 5 N 1648 2.21 5 O 1837 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ASP 652": "OD1" <-> "OD2" Residue "A ASP 681": "OD1" <-> "OD2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A GLU 772": "OE1" <-> "OE2" Residue "A ASP 779": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9929 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7662 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 939} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2100 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 240} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 37 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Unusual residues: {'NAG': 5, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.60, per 1000 atoms: 0.56 Number of scatterers: 9929 At special positions: 0 Unit cell: (82.17, 87.98, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 3 19.00 S 66 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1837 8.00 N 1648 7.00 C 6368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " 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=1, symmetry=0 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 161 " " NAG B 304 " - " ASN B 221 " " NAG B 305 " - " ASN B 193 " " NAG B 306 " - " ASN B 146 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 52.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 107 through 130 removed outlier: 3.531A pdb=" N GLU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 removed outlier: 4.230A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.917A pdb=" N SER A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 291 through 324 removed outlier: 4.251A pdb=" N TYR A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 341 Processing helix chain 'A' and resid 344 through 362 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.903A pdb=" N THR A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 376' Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.759A pdb=" N MET A 585 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 676 through 682 Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 703 through 717 removed outlier: 3.626A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 765 through 791 removed outlier: 4.117A pdb=" N LYS A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 806 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 831 through 834 Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 855 through 885 removed outlier: 3.921A pdb=" N ILE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 916 through 946 Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 961 through 981 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 994 through 1000 Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'B' and resid 33 through 66 Processing helix chain 'B' and resid 103 through 119 removed outlier: 4.685A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 6.020A pdb=" N ALA B 123 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 6.665A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.132A pdb=" N THR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.853A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.853A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.350A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE A 382 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 625 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER A 384 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET A 624 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.223A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N LEU A 592 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR A 568 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE A 594 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN A 566 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.223A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 527 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 594 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER A 529 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY A 596 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LEU A 531 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 12.328A pdb=" N VAL A 598 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 99 542 hydrogen bonds defined for protein. 1515 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: 4.11 Time building geometry restraints manager: 4.16 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: 3173 1.34 - 1.46: 1696 1.46 - 1.58: 5176 1.58 - 1.70: 2 1.70 - 1.82: 99 Bond restraints: 10146 Sorted by residual: bond pdb=" C11 PCW B 301 " pdb=" O3 PCW B 301 " ideal model delta sigma weight residual 1.326 1.450 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C31 PCW B 301 " pdb=" O2 PCW B 301 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" F3 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 10141 not shown) Histogram of bond angle deviations from ideal: 89.51 - 107.54: 406 107.54 - 125.58: 13225 125.58 - 143.62: 153 143.62 - 161.66: 0 161.66 - 179.70: 2 Bond angle restraints: 13786 Sorted by residual: angle pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " pdb=" F2 ALF A1104 " ideal model delta sigma weight residual 108.68 179.48 -70.80 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 109.63 179.70 -70.07 3.00e+00 1.11e-01 5.46e+02 angle pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " pdb=" F3 ALF A1104 " ideal model delta sigma weight residual 109.59 89.70 19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 110.21 90.39 19.82 3.00e+00 1.11e-01 4.36e+01 angle pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 109.02 89.51 19.51 3.00e+00 1.11e-01 4.23e+01 ... (remaining 13781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 6002 34.65 - 69.29: 192 69.29 - 103.94: 16 103.94 - 138.59: 0 138.59 - 173.24: 1 Dihedral angle restraints: 6211 sinusoidal: 2583 harmonic: 3628 Sorted by residual: dihedral pdb=" N PCW B 301 " pdb=" C4 PCW B 301 " pdb=" C5 PCW B 301 " pdb=" O4P PCW B 301 " ideal model delta sinusoidal sigma weight residual -66.66 106.58 -173.24 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA LEU A 376 " pdb=" C LEU A 376 " pdb=" N GLY A 377 " pdb=" CA GLY A 377 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE A 764 " pdb=" C PHE A 764 " pdb=" N ALA A 765 " pdb=" CA ALA A 765 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1421 0.074 - 0.148: 143 0.148 - 0.222: 4 0.222 - 0.296: 2 0.296 - 0.370: 1 Chirality restraints: 1571 Sorted by residual: chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 221 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1 NAG B 306 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B 306 " pdb=" O5 NAG B 306 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 221 " pdb=" N ASN B 221 " pdb=" C ASN B 221 " pdb=" CB ASN B 221 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1568 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " -0.270 2.00e-02 2.50e+03 2.26e-01 6.40e+02 pdb=" C7 NAG B 302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " 0.382 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.175 2.00e-02 2.50e+03 1.45e-01 2.61e+02 pdb=" C7 NAG B 303 " 0.049 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.233 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " 0.056 2.00e-02 2.50e+03 4.56e-02 2.60e+01 pdb=" C7 NAG B 304 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " -0.072 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.011 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.57: 54 2.57 - 3.21: 9018 3.21 - 3.85: 20178 3.85 - 4.50: 27802 4.50 - 5.14: 43895 Nonbonded interactions: 100947 Sorted by model distance: nonbonded pdb=" F2 ALF A1104 " pdb="MG MG A1105 " model vdw 1.926 2.120 nonbonded pdb=" OD1 ASP A 726 " pdb="MG MG A1105 " model vdw 2.003 2.170 nonbonded pdb=" O THR A 387 " pdb="MG MG A1105 " model vdw 2.004 2.170 nonbonded pdb=" OD2 ASP A 385 " pdb="MG MG A1105 " model vdw 2.153 2.170 nonbonded pdb=" O PRO B 145 " pdb=" OG1 THR B 148 " model vdw 2.200 3.040 ... (remaining 100942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 0.124 10146 Z= 0.268 Angle : 1.100 70.797 13786 Z= 0.427 Chirality : 0.044 0.370 1571 Planarity : 0.008 0.226 1761 Dihedral : 16.205 173.237 3864 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.85 % Allowed : 15.99 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.23), residues: 1245 helix: 1.94 (0.21), residues: 572 sheet: -0.13 (0.38), residues: 177 loop : -0.19 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.025 0.001 PHE A 300 TYR 0.016 0.001 TYR A 802 ARG 0.010 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.6777 (mtm-85) cc_final: 0.6537 (mtm-85) REVERT: A 677 MET cc_start: 0.6969 (mmp) cc_final: 0.6715 (mmt) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 1.4575 time to fit residues: 195.4417 Evaluate side-chains 121 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 35 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10146 Z= 0.250 Angle : 0.812 30.895 13786 Z= 0.353 Chirality : 0.046 0.379 1571 Planarity : 0.005 0.050 1761 Dihedral : 8.213 166.788 1575 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.14 % Allowed : 12.32 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.16 (0.23), residues: 1245 helix: 1.77 (0.21), residues: 588 sheet: 0.05 (0.42), residues: 141 loop : -0.10 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 915 HIS 0.005 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.023 0.002 TYR A 802 ARG 0.007 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 113 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6188 (mt0) REVERT: A 103 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7570 (ttp-170) REVERT: A 171 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6902 (ttmm) REVERT: A 216 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: A 414 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8207 (p0) REVERT: A 428 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.6654 (mtm-85) REVERT: A 560 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6845 (mtm-85) REVERT: A 650 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 677 MET cc_start: 0.6976 (mmp) cc_final: 0.6750 (mmt) REVERT: A 772 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 933 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (tp) REVERT: B 115 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6484 (ptt90) outliers start: 44 outliers final: 10 residues processed: 141 average time/residue: 1.4388 time to fit residues: 216.1282 Evaluate side-chains 125 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10146 Z= 0.216 Angle : 0.780 30.199 13786 Z= 0.334 Chirality : 0.044 0.295 1571 Planarity : 0.004 0.046 1761 Dihedral : 7.979 168.135 1571 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.95 % Allowed : 13.26 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.23), residues: 1245 helix: 1.88 (0.21), residues: 588 sheet: 0.15 (0.42), residues: 136 loop : -0.13 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 106 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.004 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7201 (ttmt) cc_final: 0.6911 (ttmm) REVERT: A 202 MET cc_start: 0.7219 (mmp) cc_final: 0.7004 (mtm) REVERT: A 264 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: A 428 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.6566 (mtm-85) REVERT: A 560 ARG cc_start: 0.7200 (mtm-85) cc_final: 0.6909 (mtm-85) REVERT: A 650 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8048 (m) REVERT: A 677 MET cc_start: 0.7052 (mmp) cc_final: 0.6810 (mmt) REVERT: A 682 MET cc_start: 0.7945 (mtm) cc_final: 0.7632 (ttm) REVERT: A 844 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7424 (mtt-85) REVERT: A 865 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: A 933 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8641 (tp) REVERT: B 84 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8406 (pt) REVERT: B 115 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6420 (ptt90) outliers start: 42 outliers final: 11 residues processed: 141 average time/residue: 1.4163 time to fit residues: 213.1432 Evaluate side-chains 122 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN A 884 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10146 Z= 0.174 Angle : 0.758 30.142 13786 Z= 0.321 Chirality : 0.043 0.301 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.727 168.229 1570 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.01 % Allowed : 14.02 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.36 (0.24), residues: 1245 helix: 2.05 (0.21), residues: 582 sheet: 0.18 (0.42), residues: 136 loop : -0.16 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.017 0.001 TYR A 802 ARG 0.003 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7193 (ttmt) cc_final: 0.6898 (ttmm) REVERT: A 264 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: A 428 ARG cc_start: 0.6774 (mtm-85) cc_final: 0.6564 (mtm-85) REVERT: A 560 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6932 (mtm-85) REVERT: A 677 MET cc_start: 0.7032 (mmp) cc_final: 0.6809 (mmt) REVERT: A 682 MET cc_start: 0.7999 (mtm) cc_final: 0.7686 (ttm) REVERT: A 772 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 844 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7403 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8345 (mt) REVERT: B 78 LYS cc_start: 0.8439 (mmpt) cc_final: 0.8177 (mmtm) REVERT: B 84 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8302 (pt) REVERT: B 115 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6445 (ptt90) outliers start: 32 outliers final: 14 residues processed: 123 average time/residue: 1.5004 time to fit residues: 196.2713 Evaluate side-chains 122 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10146 Z= 0.252 Angle : 0.794 30.513 13786 Z= 0.344 Chirality : 0.045 0.281 1571 Planarity : 0.005 0.047 1761 Dihedral : 7.902 172.123 1570 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.39 % Allowed : 14.02 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.19 (0.23), residues: 1245 helix: 1.85 (0.21), residues: 586 sheet: 0.08 (0.41), residues: 139 loop : -0.17 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 899 HIS 0.005 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.021 0.002 TYR A 802 ARG 0.003 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 105 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6705 (ttmt) REVERT: A 202 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7240 (ttm) REVERT: A 216 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: A 560 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6982 (mtm-85) REVERT: A 650 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8029 (m) REVERT: A 677 MET cc_start: 0.7012 (mmp) cc_final: 0.6763 (mmt) REVERT: A 772 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: A 844 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7453 (mtp-110) REVERT: A 1031 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 84 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8519 (pt) REVERT: B 115 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6453 (ptt90) outliers start: 36 outliers final: 17 residues processed: 128 average time/residue: 1.4883 time to fit residues: 202.8974 Evaluate side-chains 128 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10146 Z= 0.206 Angle : 0.772 30.304 13786 Z= 0.330 Chirality : 0.044 0.271 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.732 170.809 1570 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.39 % Allowed : 14.30 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.31 (0.23), residues: 1245 helix: 1.95 (0.21), residues: 586 sheet: 0.20 (0.41), residues: 136 loop : -0.13 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.001 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.010 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6541 (mt0) REVERT: A 171 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6677 (ttmt) REVERT: A 216 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: A 264 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: A 650 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 677 MET cc_start: 0.7007 (mmp) cc_final: 0.6784 (mmt) REVERT: A 772 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: A 844 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7453 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8340 (mt) REVERT: B 78 LYS cc_start: 0.8436 (mmpt) cc_final: 0.8181 (mmtm) REVERT: B 84 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8446 (pt) REVERT: B 115 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6404 (ptt90) REVERT: B 289 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7385 (mm-40) outliers start: 36 outliers final: 16 residues processed: 130 average time/residue: 1.4759 time to fit residues: 204.9486 Evaluate side-chains 129 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 289 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10146 Z= 0.208 Angle : 0.776 30.338 13786 Z= 0.332 Chirality : 0.044 0.253 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.617 172.352 1570 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.67 % Allowed : 14.02 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.34 (0.23), residues: 1245 helix: 1.97 (0.21), residues: 586 sheet: 0.26 (0.41), residues: 137 loop : -0.12 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.001 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.012 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 99 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6491 (mt0) REVERT: A 171 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6624 (ttmt) REVERT: A 264 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8220 (mt0) REVERT: A 650 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8005 (m) REVERT: A 677 MET cc_start: 0.7017 (mmp) cc_final: 0.6788 (mmt) REVERT: A 772 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 844 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7453 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8346 (mt) REVERT: B 78 LYS cc_start: 0.8393 (mmpt) cc_final: 0.8148 (mmtm) REVERT: B 115 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6400 (ptt90) REVERT: B 289 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7430 (mm-40) outliers start: 39 outliers final: 17 residues processed: 125 average time/residue: 1.5442 time to fit residues: 205.6291 Evaluate side-chains 123 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 289 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10146 Z= 0.201 Angle : 0.774 30.329 13786 Z= 0.330 Chirality : 0.044 0.242 1571 Planarity : 0.004 0.053 1761 Dihedral : 7.478 173.427 1570 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.20 % Allowed : 14.58 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.37 (0.24), residues: 1245 helix: 2.00 (0.21), residues: 586 sheet: 0.30 (0.42), residues: 137 loop : -0.13 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.029 0.001 PHE A 300 TYR 0.017 0.001 TYR A 802 ARG 0.012 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6608 (ttmt) REVERT: A 264 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: A 650 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7993 (m) REVERT: A 677 MET cc_start: 0.7014 (mmp) cc_final: 0.6776 (mmt) REVERT: A 682 MET cc_start: 0.8299 (mtm) cc_final: 0.7955 (mtp) REVERT: A 772 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 844 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7419 (mtt-85) REVERT: A 865 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: A 1031 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8370 (mt) REVERT: B 115 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6403 (ptt90) outliers start: 34 outliers final: 17 residues processed: 125 average time/residue: 1.5054 time to fit residues: 200.5165 Evaluate side-chains 124 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 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 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10146 Z= 0.204 Angle : 0.777 30.349 13786 Z= 0.332 Chirality : 0.044 0.230 1571 Planarity : 0.004 0.054 1761 Dihedral : 7.476 174.254 1570 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.63 % Allowed : 15.24 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.34 (0.24), residues: 1245 helix: 1.98 (0.21), residues: 586 sheet: 0.25 (0.42), residues: 138 loop : -0.13 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.029 0.001 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.013 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6832 (ttmm) REVERT: A 264 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: A 650 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 677 MET cc_start: 0.7004 (mmp) cc_final: 0.6765 (mmt) REVERT: A 682 MET cc_start: 0.8289 (mtm) cc_final: 0.7925 (mtp) REVERT: A 772 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: A 844 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7446 (mtt-85) REVERT: A 865 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: A 1031 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 78 LYS cc_start: 0.8349 (mmpt) cc_final: 0.8122 (mmtm) REVERT: B 115 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6396 (ptt90) outliers start: 28 outliers final: 14 residues processed: 119 average time/residue: 1.4790 time to fit residues: 187.0321 Evaluate side-chains 120 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10146 Z= 0.212 Angle : 0.784 30.412 13786 Z= 0.335 Chirality : 0.044 0.228 1571 Planarity : 0.005 0.062 1761 Dihedral : 7.492 174.621 1570 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.54 % Allowed : 15.52 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.34 (0.23), residues: 1245 helix: 1.97 (0.21), residues: 586 sheet: 0.28 (0.42), residues: 138 loop : -0.12 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.014 0.000 ARG A 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6834 (ttmm) REVERT: A 264 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: A 650 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 677 MET cc_start: 0.7017 (mmp) cc_final: 0.6772 (mmt) REVERT: A 682 MET cc_start: 0.8300 (mtm) cc_final: 0.7947 (mtp) REVERT: A 772 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: A 844 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7452 (mtt-85) REVERT: A 865 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: A 1031 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8363 (mt) REVERT: B 78 LYS cc_start: 0.8391 (mmpt) cc_final: 0.8141 (mmtm) REVERT: B 115 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6409 (ptt90) outliers start: 27 outliers final: 17 residues processed: 118 average time/residue: 1.4658 time to fit residues: 184.1019 Evaluate side-chains 122 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 289 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 188 GLN A 446 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108149 restraints weight = 10993.186| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.82 r_work: 0.3113 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10146 Z= 0.208 Angle : 0.782 30.395 13786 Z= 0.334 Chirality : 0.044 0.230 1571 Planarity : 0.005 0.063 1761 Dihedral : 7.509 175.244 1570 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.45 % Allowed : 15.80 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.34 (0.23), residues: 1245 helix: 1.97 (0.21), residues: 586 sheet: 0.23 (0.41), residues: 138 loop : -0.11 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.001 PHE A 300 TYR 0.018 0.001 TYR A 802 ARG 0.014 0.000 ARG A 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3982.58 seconds wall clock time: 71 minutes 31.19 seconds (4291.19 seconds total)