Starting phenix.real_space_refine on Sat Nov 16 12:48:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/11_2024/8ijv_35500.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/11_2024/8ijv_35500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/11_2024/8ijv_35500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/11_2024/8ijv_35500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/11_2024/8ijv_35500.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/11_2024/8ijv_35500.cif" } resolution = 2.1 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= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 65 5.16 5 Cl 4 4.86 5 Be 1 3.05 5 C 6570 2.51 5 N 1654 2.21 5 O 2229 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10532 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7631 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 47, 'TRANS': 935} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2142 Classifications: {'peptide': 268} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245} Chain: "A" Number of atoms: 238 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 216 Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 6, 216 Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 189 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'CLR': 2, 'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 255 Classifications: {'water': 255} Link IDs: {None: 254} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01APWI A1106 " occ=0.46 ... (42 atoms not shown) pdb="CL2 BPWI A1106 " occ=0.54 Time building chain proxies: 7.75, per 1000 atoms: 0.74 Number of scatterers: 10532 At special positions: 0 Unit cell: (81.216, 97.76, 174.464, 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) Cl 4 17.00 S 65 16.00 P 5 15.00 Mg 1 11.99 F 3 9.00 O 2229 8.00 N 1654 7.00 C 6570 6.00 Be 1 4.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 130 " " NAG B 304 " - " ASN B 161 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 50.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.614A pdb=" N LYS A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 129 Processing helix chain 'A' and resid 135 through 170 removed outlier: 3.989A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' 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 322 Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 344 through 362 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.561A pdb=" N SER A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) 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 483 Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.664A pdb=" N ARG A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 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 removed outlier: 3.580A pdb=" N ASP A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' 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: 4.072A pdb=" N LYS A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 806 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 812 through 820 Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.608A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 865 through 885 Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 916 through 946 removed outlier: 3.622A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) 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 removed outlier: 3.861A pdb=" N TRP A 998 " --> pdb=" O ARG A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'B' and resid 34 through 66 Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.240A pdb=" N TRP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 6.664A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.117A 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 185 through 190 removed outlier: 11.763A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET A 257 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 221 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 261 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 219 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 263 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 217 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 265 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 215 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 11.763A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET A 257 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 221 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 261 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 219 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 263 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 217 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 265 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 215 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.323A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.245A 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: 5.334A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 512 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 497 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 491 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 487 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.359A 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: 5.334A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER A 529 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLY A 596 " --> pdb=" O SER A 529 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.697A pdb=" N ALA A 441 " --> pdb=" O ILE A 457 " (cutoff:3.500A) 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 28 through 29 Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AB1, first strand: chain 'B' and resid 94 through 99 removed outlier: 4.493A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1509 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: 4.22 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1623 1.29 - 1.42: 2593 1.42 - 1.55: 6056 1.55 - 1.68: 17 1.68 - 1.82: 101 Bond restraints: 10390 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.764 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.753 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.752 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.447 -0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" C17APWI A1106 " pdb=" N01APWI A1106 " ideal model delta sigma weight residual 1.466 1.292 0.174 2.00e-02 2.50e+03 7.56e+01 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 14001 5.50 - 10.99: 64 10.99 - 16.49: 9 16.49 - 21.98: 3 21.98 - 27.48: 5 Bond angle restraints: 14082 Sorted by residual: angle pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C9 CLR B 306 " ideal model delta sigma weight residual 111.86 84.38 27.48 3.00e+00 1.11e-01 8.39e+01 angle pdb=" C1 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C19 CLR B 306 " ideal model delta sigma weight residual 109.60 82.90 26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C5 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 111.64 86.86 24.78 3.00e+00 1.11e-01 6.82e+01 angle pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C5 CLR B 306 " ideal model delta sigma weight residual 108.37 83.64 24.73 3.00e+00 1.11e-01 6.79e+01 angle pdb=" C6 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 109.11 86.89 22.22 3.00e+00 1.11e-01 5.48e+01 ... (remaining 14077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 6119 35.95 - 71.90: 265 71.90 - 107.85: 24 107.85 - 143.81: 6 143.81 - 179.76: 6 Dihedral angle restraints: 6420 sinusoidal: 2787 harmonic: 3633 Sorted by residual: dihedral pdb=" C13BPWI A1106 " pdb=" C14BPWI A1106 " pdb=" O01BPWI A1106 " pdb=" C15BPWI A1106 " ideal model delta sinusoidal sigma weight residual -179.86 -0.10 -179.76 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C5 CLR B 306 " pdb=" C6 CLR B 306 " ideal model delta sinusoidal sigma weight residual 252.42 74.68 177.74 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C9 CLR B 306 " pdb=" C19 CLR B 306 " ideal model delta sinusoidal sigma weight residual 51.90 -124.69 176.59 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 1573 0.358 - 0.716: 0 0.716 - 1.074: 0 1.074 - 1.432: 0 1.432 - 1.790: 1 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C10 CLR B 306 " pdb=" C1 CLR B 306 " pdb=" C5 CLR B 306 " pdb=" C9 CLR B 306 " both_signs ideal model delta sigma weight residual False -2.85 -1.06 -1.79 2.00e-01 2.50e+01 8.01e+01 chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1571 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 130 " 0.216 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" CG ASN B 130 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN B 130 " -0.148 2.00e-02 2.50e+03 pdb=" ND2 ASN B 130 " -0.230 2.00e-02 2.50e+03 pdb=" C1 NAG B 303 " 0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01APWI A1106 " 0.006 2.00e-02 2.50e+03 5.57e-02 6.98e+01 pdb=" C07APWI A1106 " 0.000 2.00e-02 2.50e+03 pdb=" C08APWI A1106 " 0.048 2.00e-02 2.50e+03 pdb=" C09APWI A1106 " 0.101 2.00e-02 2.50e+03 pdb=" C10APWI A1106 " 0.043 2.00e-02 2.50e+03 pdb=" C11APWI A1106 " -0.014 2.00e-02 2.50e+03 pdb=" C12APWI A1106 " -0.027 2.00e-02 2.50e+03 pdb=" C13APWI A1106 " -0.089 2.00e-02 2.50e+03 pdb="CL2 APWI A1106 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01APWI A1106 " -0.028 2.00e-02 2.50e+03 4.56e-02 4.16e+01 pdb=" C02APWI A1106 " -0.045 2.00e-02 2.50e+03 pdb=" C03APWI A1106 " -0.016 2.00e-02 2.50e+03 pdb=" C04APWI A1106 " -0.001 2.00e-02 2.50e+03 pdb=" C05APWI A1106 " -0.026 2.00e-02 2.50e+03 pdb=" C06APWI A1106 " -0.036 2.00e-02 2.50e+03 pdb=" C07APWI A1106 " 0.089 2.00e-02 2.50e+03 pdb="CL1 APWI A1106 " 0.062 2.00e-02 2.50e+03 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 129 2.56 - 3.14: 8347 3.14 - 3.73: 17964 3.73 - 4.31: 25929 4.31 - 4.90: 39940 Nonbonded interactions: 92309 Sorted by model distance: nonbonded pdb=" O THR A 387 " pdb="MG MG A1102 " model vdw 1.973 2.170 nonbonded pdb="MG MG A1102 " pdb=" O HOH A1204 " model vdw 2.021 2.170 nonbonded pdb=" F2 BFD A 385 " pdb="MG MG A1102 " model vdw 2.104 2.120 nonbonded pdb=" CE LYS B 135 " pdb=" O HOH B 463 " model vdw 2.141 3.440 nonbonded pdb=" F1 BFD A 385 " pdb=" OG1 THR A 626 " model vdw 2.152 2.990 ... (remaining 92304 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=0.46 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.770 Find NCS groups from input model: 0.140 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.008 0.235 10390 Z= 0.538 Angle : 1.098 27.477 14082 Z= 0.472 Chirality : 0.066 1.790 1574 Planarity : 0.006 0.125 1777 Dihedral : 20.105 179.758 4071 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.73 % Allowed : 17.78 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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 (0.24), residues: 1244 helix: 1.65 (0.22), residues: 579 sheet: 0.43 (0.41), residues: 155 loop : -0.04 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.022 0.002 PHE A 333 TYR 0.017 0.001 TYR A 802 ARG 0.006 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 29 residues processed: 145 average time/residue: 1.5244 time to fit residues: 236.0955 Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10390 Z= 0.175 Angle : 0.701 31.047 14082 Z= 0.322 Chirality : 0.063 1.800 1574 Planarity : 0.005 0.057 1777 Dihedral : 17.619 176.881 1831 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.76 % Allowed : 15.52 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1244 helix: 1.80 (0.22), residues: 587 sheet: 0.48 (0.41), residues: 154 loop : -0.01 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.014 0.001 PHE A 161 TYR 0.020 0.001 TYR A 802 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7936 (mp10) cc_final: 0.7675 (mm-40) REVERT: A 247 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: A 505 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5516 (tp30) REVERT: A 835 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7681 (mttp) REVERT: A 844 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7755 (mtt-85) REVERT: B 78 LYS cc_start: 0.8601 (mmtp) cc_final: 0.7983 (mmmt) REVERT: B 135 LYS cc_start: 0.7578 (tptm) cc_final: 0.7107 (mmpt) outliers start: 40 outliers final: 21 residues processed: 144 average time/residue: 1.5273 time to fit residues: 235.3846 Evaluate side-chains 135 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10390 Z= 0.170 Angle : 0.689 30.868 14082 Z= 0.315 Chirality : 0.063 1.812 1574 Planarity : 0.004 0.054 1777 Dihedral : 17.354 176.481 1809 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.39 % Allowed : 15.15 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.41 (0.24), residues: 1244 helix: 1.93 (0.22), residues: 581 sheet: 0.69 (0.41), residues: 150 loop : -0.10 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.028 0.001 PHE A 970 TYR 0.021 0.001 TYR A 802 ARG 0.004 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7933 (mp10) cc_final: 0.7639 (mm-40) REVERT: A 247 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: A 835 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7663 (mttp) REVERT: A 844 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7756 (mtt-85) REVERT: B 78 LYS cc_start: 0.8601 (mmtp) cc_final: 0.7972 (mmmt) REVERT: B 135 LYS cc_start: 0.7570 (tptm) cc_final: 0.7054 (mmpt) outliers start: 36 outliers final: 24 residues processed: 139 average time/residue: 1.5807 time to fit residues: 233.9918 Evaluate side-chains 136 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 665 ASN A 792 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10390 Z= 0.241 Angle : 0.744 31.244 14082 Z= 0.349 Chirality : 0.065 1.823 1574 Planarity : 0.005 0.053 1777 Dihedral : 17.288 178.125 1808 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.95 % Allowed : 14.77 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.22 (0.23), residues: 1244 helix: 1.71 (0.21), residues: 587 sheet: 0.50 (0.41), residues: 151 loop : -0.08 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 997 HIS 0.005 0.001 HIS B 227 PHE 0.017 0.002 PHE A 315 TYR 0.023 0.002 TYR A 802 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7942 (mp10) cc_final: 0.7636 (mm-40) REVERT: A 247 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: A 453 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7931 (mttp) REVERT: A 835 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7718 (mttp) REVERT: A 844 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7785 (mtt-85) REVERT: B 78 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8001 (mmmt) outliers start: 42 outliers final: 28 residues processed: 145 average time/residue: 1.5087 time to fit residues: 233.6363 Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.0050 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10390 Z= 0.241 Angle : 0.744 31.244 14082 Z= 0.349 Chirality : 0.065 1.823 1574 Planarity : 0.005 0.053 1777 Dihedral : 17.294 178.125 1804 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.01 % Allowed : 15.90 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.22 (0.23), residues: 1244 helix: 1.71 (0.21), residues: 587 sheet: 0.50 (0.41), residues: 151 loop : -0.08 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 997 HIS 0.005 0.001 HIS B 227 PHE 0.017 0.002 PHE A 315 TYR 0.023 0.002 TYR A 802 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7943 (mp10) cc_final: 0.7636 (mm-40) REVERT: A 247 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: A 453 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7931 (mttp) REVERT: A 835 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7718 (mttp) REVERT: A 844 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7785 (mtt-85) REVERT: B 78 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8001 (mmmt) outliers start: 32 outliers final: 28 residues processed: 134 average time/residue: 1.5376 time to fit residues: 220.2752 Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL 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: 2.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10390 Z= 0.168 Angle : 0.685 30.637 14082 Z= 0.313 Chirality : 0.063 1.812 1574 Planarity : 0.004 0.052 1777 Dihedral : 17.032 176.569 1804 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.20 % Allowed : 15.33 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.40 (0.24), residues: 1244 helix: 1.93 (0.22), residues: 581 sheet: 0.66 (0.40), residues: 150 loop : -0.08 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.028 0.001 PHE A 970 TYR 0.020 0.001 TYR A 802 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5886 (m-40) REVERT: A 130 GLU cc_start: 0.5809 (pp20) cc_final: 0.5309 (pp20) REVERT: A 247 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: A 505 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5684 (pt0) REVERT: A 560 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6847 (tpt90) REVERT: A 844 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: B 78 LYS cc_start: 0.8622 (mmtp) cc_final: 0.7987 (mmmt) REVERT: B 135 LYS cc_start: 0.7500 (tptm) cc_final: 0.6941 (mmpt) outliers start: 34 outliers final: 23 residues processed: 139 average time/residue: 1.5676 time to fit residues: 232.7886 Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.0670 chunk 74 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10390 Z= 0.168 Angle : 0.685 30.637 14082 Z= 0.313 Chirality : 0.063 1.812 1574 Planarity : 0.004 0.052 1777 Dihedral : 16.955 176.569 1797 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.63 % Allowed : 16.09 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.40 (0.24), residues: 1244 helix: 1.93 (0.22), residues: 581 sheet: 0.66 (0.40), residues: 150 loop : -0.08 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.028 0.001 PHE A 970 TYR 0.020 0.001 TYR A 802 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5886 (m-40) REVERT: A 130 GLU cc_start: 0.5693 (pp20) cc_final: 0.5308 (pp20) REVERT: A 247 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: A 505 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5684 (pt0) REVERT: A 560 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6846 (tpt90) REVERT: A 844 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: B 78 LYS cc_start: 0.8622 (mmtp) cc_final: 0.7987 (mmmt) REVERT: B 135 LYS cc_start: 0.7500 (tptm) cc_final: 0.6941 (mmpt) outliers start: 28 outliers final: 23 residues processed: 132 average time/residue: 1.5825 time to fit residues: 222.8792 Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10390 Z= 0.170 Angle : 0.685 30.636 14082 Z= 0.313 Chirality : 0.063 1.812 1574 Planarity : 0.004 0.052 1777 Dihedral : 16.974 176.571 1797 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.63 % Allowed : 16.09 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.41 (0.24), residues: 1244 helix: 1.93 (0.22), residues: 581 sheet: 0.66 (0.40), residues: 150 loop : -0.08 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.026 0.001 PHE A 970 TYR 0.020 0.001 TYR A 802 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5886 (m-40) REVERT: A 130 GLU cc_start: 0.5693 (pp20) cc_final: 0.5307 (pp20) REVERT: A 247 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: A 505 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5684 (pt0) REVERT: A 560 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6847 (tpt90) REVERT: A 844 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: B 78 LYS cc_start: 0.8622 (mmtp) cc_final: 0.7987 (mmmt) REVERT: B 135 LYS cc_start: 0.7500 (tptm) cc_final: 0.6941 (mmpt) outliers start: 28 outliers final: 23 residues processed: 132 average time/residue: 1.5168 time to fit residues: 213.8062 Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL 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: 0.8980 chunk 111 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 chunk 73 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10390 Z= 0.172 Angle : 0.687 30.622 14082 Z= 0.315 Chirality : 0.064 1.817 1574 Planarity : 0.004 0.051 1777 Dihedral : 16.807 176.367 1797 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.82 % Allowed : 15.99 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.42 (0.24), residues: 1244 helix: 1.93 (0.22), residues: 581 sheet: 0.79 (0.41), residues: 147 loop : -0.10 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.021 0.001 PHE A 333 TYR 0.020 0.001 TYR A 802 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.6273 (OUTLIER) cc_final: 0.5883 (m-40) REVERT: A 130 GLU cc_start: 0.5899 (pp20) cc_final: 0.5413 (pp20) REVERT: A 247 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: A 560 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6830 (tpt90) REVERT: A 689 GLU cc_start: 0.7676 (tp30) cc_final: 0.7353 (tp30) REVERT: A 844 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7756 (mtt-85) REVERT: A 904 LEU cc_start: 0.8487 (mt) cc_final: 0.8127 (tp) REVERT: B 78 LYS cc_start: 0.8632 (mmtp) cc_final: 0.7994 (mmmt) REVERT: B 135 LYS cc_start: 0.7515 (tptm) cc_final: 0.6986 (mmpt) outliers start: 30 outliers final: 24 residues processed: 139 average time/residue: 1.4976 time to fit residues: 222.5188 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL 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: 5.9990 chunk 55 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 98 optimal weight: 0.0570 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10390 Z= 0.156 Angle : 0.677 30.509 14082 Z= 0.307 Chirality : 0.063 1.813 1574 Planarity : 0.004 0.051 1777 Dihedral : 16.684 176.234 1797 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.82 % Allowed : 15.71 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.49 (0.24), residues: 1244 helix: 1.99 (0.22), residues: 581 sheet: 0.83 (0.41), residues: 147 loop : -0.07 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.039 0.001 PHE A 970 TYR 0.019 0.001 TYR A 802 ARG 0.004 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.6297 (OUTLIER) cc_final: 0.5908 (m-40) REVERT: A 193 GLN cc_start: 0.7931 (mp10) cc_final: 0.7600 (mm-40) REVERT: A 247 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: A 560 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6822 (tpt90) REVERT: A 689 GLU cc_start: 0.7654 (tp30) cc_final: 0.7326 (tp30) REVERT: A 844 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7762 (mtt-85) REVERT: A 904 LEU cc_start: 0.8473 (mt) cc_final: 0.8125 (tp) REVERT: B 78 LYS cc_start: 0.8614 (mmtp) cc_final: 0.7979 (mmmt) REVERT: B 135 LYS cc_start: 0.7474 (tptm) cc_final: 0.6961 (mmpt) outliers start: 30 outliers final: 22 residues processed: 136 average time/residue: 1.5626 time to fit residues: 227.4066 Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121492 restraints weight = 9462.301| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.55 r_work: 0.3159 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10390 Z= 0.173 Angle : 0.689 30.533 14082 Z= 0.315 Chirality : 0.064 1.819 1574 Planarity : 0.004 0.051 1777 Dihedral : 16.630 176.195 1797 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.35 % Allowed : 16.18 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.47 (0.24), residues: 1244 helix: 1.96 (0.22), residues: 581 sheet: 0.83 (0.41), residues: 147 loop : -0.06 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.004 0.001 HIS B 227 PHE 0.022 0.002 PHE A 333 TYR 0.019 0.001 TYR A 802 ARG 0.004 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4875.54 seconds wall clock time: 88 minutes 43.23 seconds (5323.23 seconds total)