Starting phenix.real_space_refine on Mon Jul 22 13:38:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/07_2024/8wa5_37391_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/07_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_37391/07_2024/8wa5_37391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/07_2024/8wa5_37391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/07_2024/8wa5_37391_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/07_2024/8wa5_37391_neut.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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 8.26, per 1000 atoms: 0.83 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: 4.46 Conformation dependent library (CDL) restraints added in 2.3 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: 1.28 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: 3.86 Time building geometry restraints manager: 4.61 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 2.440 ... (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 ========== 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: 3.690 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 34.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.210 ------------------------------------------------------------------------------- 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 : 1.178 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: 1.4619 time to fit residues: 196.0930 Evaluate side-chains 121 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.0746 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= 0.218 Angle : 0.791 30.320 13786 Z= 0.339 Chirality : 0.045 0.420 1571 Planarity : 0.005 0.049 1761 Dihedral : 8.048 165.736 1575 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.05 % Allowed : 12.61 % Favored : 83.35 % 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: 1.23 (0.23), residues: 1245 helix: 1.82 (0.21), residues: 589 sheet: 0.07 (0.42), residues: 141 loop : -0.06 (0.27), residues: 515 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 0.028 0.002 PHE A 300 TYR 0.021 0.001 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 154 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6114 (mt0) REVERT: A 103 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7584 (ttp-170) REVERT: A 216 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: A 414 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8119 (p0) REVERT: A 560 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6960 (mtm-85) REVERT: A 650 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 677 MET cc_start: 0.6956 (mmp) cc_final: 0.6720 (mmt) REVERT: A 772 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: A 933 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 115 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6499 (ptt90) outliers start: 43 outliers final: 10 residues processed: 137 average time/residue: 1.4045 time to fit residues: 205.1053 Evaluate side-chains 126 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 560 ARG 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: 4.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.0570 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10146 Z= 0.285 Angle : 0.810 30.802 13786 Z= 0.353 Chirality : 0.046 0.293 1571 Planarity : 0.005 0.049 1761 Dihedral : 8.098 170.395 1571 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.14 % Allowed : 13.08 % 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: 1.13 (0.23), residues: 1245 helix: 1.77 (0.21), residues: 587 sheet: -0.01 (0.42), residues: 139 loop : -0.15 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 106 HIS 0.006 0.001 HIS A 629 PHE 0.030 0.002 PHE A 300 TYR 0.021 0.002 TYR A 802 ARG 0.009 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 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6287 (mt0) REVERT: A 171 LYS cc_start: 0.7228 (ttmt) cc_final: 0.6947 (ttmm) REVERT: A 216 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: A 264 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: A 414 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8260 (p0) REVERT: A 650 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 677 MET cc_start: 0.7002 (mmp) cc_final: 0.6751 (mmt) REVERT: A 844 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7442 (mtt-85) REVERT: A 933 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8653 (tp) REVERT: B 84 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8539 (pt) REVERT: B 115 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6426 (ptt90) outliers start: 44 outliers final: 16 residues processed: 144 average time/residue: 1.4264 time to fit residues: 218.8485 Evaluate side-chains 136 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN 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 262 THR Chi-restraints excluded: chain A residue 264 GLN 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 585 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 680 LYS 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 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: 0.4980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.0770 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 GLN B 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10146 Z= 0.165 Angle : 0.754 30.309 13786 Z= 0.319 Chirality : 0.043 0.301 1571 Planarity : 0.004 0.044 1761 Dihedral : 7.778 167.459 1571 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.20 % Allowed : 14.11 % Favored : 82.69 % 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: 1.33 (0.24), residues: 1245 helix: 1.99 (0.22), residues: 587 sheet: 0.08 (0.42), residues: 139 loop : -0.12 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 915 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.015 0.001 TYR A 802 ARG 0.008 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 143 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6860 (ttmm) REVERT: A 264 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: A 414 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (p0) REVERT: A 560 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.7078 (mtm-85) REVERT: A 677 MET cc_start: 0.6983 (mmp) cc_final: 0.6762 (mmt) REVERT: A 772 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 1031 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8363 (mt) REVERT: B 84 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8320 (pt) REVERT: B 115 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6443 (ptt90) outliers start: 34 outliers final: 10 residues processed: 130 average time/residue: 1.4917 time to fit residues: 205.9984 Evaluate side-chains 121 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 656 ARG 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 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 106 TRP Chi-restraints excluded: chain B residue 115 ARG 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: 0.6980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8242 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10146 Z= 0.228 Angle : 0.781 30.817 13786 Z= 0.335 Chirality : 0.044 0.269 1571 Planarity : 0.004 0.047 1761 Dihedral : 7.766 170.913 1570 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.39 % Allowed : 14.49 % 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: 1.26 (0.24), residues: 1245 helix: 1.92 (0.21), residues: 586 sheet: 0.07 (0.41), residues: 139 loop : -0.13 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.028 0.002 PHE A 300 TYR 0.020 0.001 TYR A 802 ARG 0.009 0.000 ARG A 428 *********************** 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 148 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6891 (ttmm) REVERT: A 202 MET cc_start: 0.7216 (mmp) cc_final: 0.6939 (ttm) REVERT: A 264 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: A 414 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8310 (p0) REVERT: A 677 MET cc_start: 0.6958 (mmp) cc_final: 0.6750 (mmt) REVERT: A 772 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 844 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7445 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 78 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8145 (mmtm) REVERT: B 84 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8477 (pt) REVERT: B 115 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6462 (ptt90) outliers start: 36 outliers final: 15 residues processed: 134 average time/residue: 1.4647 time to fit residues: 208.8516 Evaluate side-chains 129 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain A residue 264 GLN 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 656 ARG 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 78 LYS 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 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.8279 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10146 Z= 0.339 Angle : 0.833 31.835 13786 Z= 0.367 Chirality : 0.048 0.271 1571 Planarity : 0.005 0.049 1761 Dihedral : 8.180 174.785 1570 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.95 % Allowed : 13.83 % 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: 1.02 (0.23), residues: 1245 helix: 1.70 (0.21), residues: 586 sheet: -0.02 (0.39), residues: 157 loop : -0.23 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 401 HIS 0.006 0.001 HIS A 629 PHE 0.031 0.002 PHE A 300 TYR 0.021 0.002 TYR A 802 ARG 0.009 0.001 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 152 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 110 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6510 (mt0) REVERT: A 171 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7031 (ttmm) REVERT: A 176 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: A 216 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: A 264 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: A 455 ILE cc_start: 0.8545 (mm) cc_final: 0.8316 (mm) REVERT: A 560 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6972 (mtm-85) REVERT: A 650 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8015 (m) REVERT: A 739 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8686 (tt) REVERT: A 772 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: A 844 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7459 (mtp-110) REVERT: A 1002 MET cc_start: 0.8645 (mtt) cc_final: 0.8210 (mtt) REVERT: A 1031 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8474 (mt) REVERT: B 84 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8652 (pt) REVERT: B 115 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6452 (ptt90) outliers start: 42 outliers final: 16 residues processed: 135 average time/residue: 1.4204 time to fit residues: 205.2126 Evaluate side-chains 131 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 176 GLN 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 262 THR 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 461 SER Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 739 ILE 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 1005 SER 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 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 0.0870 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10146 Z= 0.156 Angle : 0.756 30.356 13786 Z= 0.319 Chirality : 0.043 0.291 1571 Planarity : 0.004 0.047 1761 Dihedral : 7.617 170.902 1570 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.92 % Allowed : 15.33 % 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: 1.30 (0.24), residues: 1245 helix: 2.01 (0.22), residues: 586 sheet: 0.06 (0.41), residues: 138 loop : -0.19 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.015 0.001 TYR A 802 ARG 0.013 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 134 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6664 (ttmt) REVERT: A 176 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: A 202 MET cc_start: 0.7228 (ttm) cc_final: 0.7009 (ttm) REVERT: A 264 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: A 455 ILE cc_start: 0.8561 (mm) cc_final: 0.8360 (mp) REVERT: A 485 LYS cc_start: 0.6548 (ptpt) cc_final: 0.6016 (pttp) REVERT: A 677 MET cc_start: 0.6956 (mmp) cc_final: 0.6707 (mmt) REVERT: A 844 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7433 (mtt-85) REVERT: A 1002 MET cc_start: 0.8598 (mtt) cc_final: 0.8169 (mtt) REVERT: A 1031 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8370 (mt) REVERT: B 78 LYS cc_start: 0.8397 (mmpt) cc_final: 0.8154 (mmtm) REVERT: B 115 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6394 (ptt90) outliers start: 31 outliers final: 11 residues processed: 122 average time/residue: 1.4991 time to fit residues: 194.7074 Evaluate side-chains 117 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 656 ARG 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8238 moved from start: 0.1666 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= 0.189 Angle : 0.769 30.456 13786 Z= 0.326 Chirality : 0.044 0.249 1571 Planarity : 0.004 0.048 1761 Dihedral : 7.515 172.813 1570 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.26 % Allowed : 15.99 % 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: 1.33 (0.24), residues: 1245 helix: 2.00 (0.22), residues: 586 sheet: 0.16 (0.41), residues: 140 loop : -0.16 (0.26), residues: 519 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 0.028 0.001 PHE A 300 TYR 0.018 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 127 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6694 (ttmt) REVERT: A 176 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: A 216 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: A 264 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: A 677 MET cc_start: 0.6994 (mmp) cc_final: 0.6725 (mmt) REVERT: A 844 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7416 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 78 LYS cc_start: 0.8369 (mmpt) cc_final: 0.8163 (mmtm) REVERT: B 115 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6384 (ptt90) outliers start: 24 outliers final: 12 residues processed: 117 average time/residue: 1.6356 time to fit residues: 203.6527 Evaluate side-chains 121 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 683 ASP 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 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 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: 0.6980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8245 moved from start: 0.1713 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= 0.207 Angle : 0.776 30.650 13786 Z= 0.331 Chirality : 0.044 0.239 1571 Planarity : 0.005 0.059 1761 Dihedral : 7.469 172.940 1570 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.35 % Allowed : 16.27 % Favored : 81.37 % 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: 1.30 (0.24), residues: 1245 helix: 1.97 (0.22), residues: 586 sheet: 0.18 (0.42), residues: 140 loop : -0.17 (0.26), residues: 519 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 0.018 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 130 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6901 (ttmm) REVERT: A 176 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: A 216 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: A 264 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: A 521 GLU cc_start: 0.7007 (pm20) cc_final: 0.6720 (pm20) REVERT: A 650 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7959 (m) REVERT: A 677 MET cc_start: 0.7013 (mmp) cc_final: 0.6742 (mmt) REVERT: A 844 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7465 (mtp-110) REVERT: A 1031 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8412 (mt) REVERT: B 78 LYS cc_start: 0.8359 (mmpt) cc_final: 0.8145 (mmtm) REVERT: B 115 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6410 (ptt90) outliers start: 25 outliers final: 14 residues processed: 120 average time/residue: 1.4691 time to fit residues: 187.5880 Evaluate side-chains 127 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 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 650 VAL Chi-restraints excluded: chain A residue 656 ARG 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 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 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 141 SER 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 117 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.8237 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10146 Z= 0.190 Angle : 0.769 30.489 13786 Z= 0.326 Chirality : 0.044 0.229 1571 Planarity : 0.004 0.061 1761 Dihedral : 7.377 172.933 1570 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.35 % Allowed : 16.37 % Favored : 81.28 % 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: 1.33 (0.24), residues: 1245 helix: 2.01 (0.22), residues: 586 sheet: 0.18 (0.41), residues: 140 loop : -0.18 (0.26), residues: 519 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 0.028 0.001 PHE A 300 TYR 0.017 0.001 TYR A 802 ARG 0.015 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 129 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6893 (ttmm) REVERT: A 216 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: A 264 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: A 650 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7949 (m) REVERT: A 677 MET cc_start: 0.7048 (mmp) cc_final: 0.6783 (mmt) REVERT: A 844 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7423 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8408 (mt) REVERT: B 115 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6772 (ptt90) outliers start: 25 outliers final: 14 residues processed: 119 average time/residue: 1.5042 time to fit residues: 190.2693 Evaluate side-chains 119 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 683 ASP 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 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 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 141 SER 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 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 18 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 405 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109259 restraints weight = 10995.236| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.82 r_work: 0.3123 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10146 Z= 0.179 Angle : 0.764 30.408 13786 Z= 0.323 Chirality : 0.043 0.220 1571 Planarity : 0.004 0.062 1761 Dihedral : 7.295 172.893 1570 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.16 % Allowed : 17.03 % Favored : 80.81 % 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: 2.03 (0.22), residues: 586 sheet: 0.20 (0.41), residues: 140 loop : -0.17 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.016 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: 4057.77 seconds wall clock time: 72 minutes 32.94 seconds (4352.94 seconds total)