Starting phenix.real_space_refine on Fri Mar 15 02:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijl_35488/03_2024/8ijl_35488_updated.pdb" } resolution = 2.62 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= -0.000 sd= 0.034 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 Al 1 5.89 5 P 7 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Na 2 4.78 5 C 6731 2.51 5 N 1643 2.21 5 O 1924 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 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ASP 223": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10360 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7638 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 946} Chain: "B" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2165 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 247} Chain breaks: 1 Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 429 Unusual residues: {' MG': 1, ' NA': 2, 'ADP': 1, 'ALF': 1, 'CLR': 1, 'PCW': 5, 'Q7G': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'CLR': 1, 'NAG': 1, 'Q7G': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 41 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 6.01, per 1000 atoms: 0.58 Number of scatterers: 10360 At special positions: 0 Unit cell: (75.53, 89.64, 175.13, 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) S 47 16.00 P 7 15.00 Al 1 13.00 Mg 1 11.99 Na 2 11.00 F 4 9.00 O 1924 8.00 N 1643 7.00 C 6731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " 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 401 " - " ASN B 158 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 10 sheets defined 42.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.680A pdb=" N THR A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 removed outlier: 3.776A pdb=" N GLN A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 Processing helix chain 'A' and resid 141 through 162 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 295 through 325 removed outlier: 3.663A pdb=" N ALA A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.626A pdb=" N LYS A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 4.803A pdb=" N LEU A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 380 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 439 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 463 through 476 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.558A pdb=" N SER A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 660 removed outlier: 3.564A pdb=" N ALA A 657 " --> pdb=" O VAL A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.769A pdb=" N GLN A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 767 through 808 removed outlier: 3.655A pdb=" N PHE A 781 " --> pdb=" O ARG A 778 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 784 " --> pdb=" O PHE A 781 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 785 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 793 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 796 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS A 800 " --> pdb=" O ALA A 797 " (cutoff:3.500A) Proline residue: A 801 - end of helix removed outlier: 3.632A pdb=" N VAL A 807 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 808 " --> pdb=" O TYR A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.625A pdb=" N LEU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 822 " --> pdb=" O THR A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 removed outlier: 4.008A pdb=" N ALA A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 869 through 886 removed outlier: 3.540A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 902 No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 920 through 950 removed outlier: 3.571A pdb=" N ALA A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 959 No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 965 through 983 Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1005 through 1024 Processing helix chain 'A' and resid 1029 through 1034 Processing helix chain 'B' and resid 29 through 60 removed outlier: 3.529A pdb=" N TRP B 32 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.834A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing sheet with id= A, first strand: chain 'A' and resid 188 through 193 removed outlier: 4.561A pdb=" N LEU A 182 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 202 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.332A pdb=" N CYS A 223 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP A 226 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS A 261 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.549A pdb=" N MET A 746 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS A 624 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 387 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 626 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.754A pdb=" N SER A 602 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 403 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 600 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE A 405 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL A 598 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE A 567 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 600 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 565 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 602 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG A 563 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 515 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU A 506 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 488 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 538 through 541 removed outlier: 7.076A pdb=" N PHE A 595 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 533 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N PHE A 597 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE A 535 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 674 through 678 removed outlier: 6.635A pdb=" N GLU A 699 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL A 677 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 701 " --> pdb=" O VAL A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 214 through 217 removed outlier: 6.176A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 77 through 80 Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 removed outlier: 7.899A pdb=" N ILE B 88 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS B 299 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE B 90 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU B 301 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 209 through 211 405 hydrogen bonds defined for protein. 990 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: 3.97 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1644 1.32 - 1.44: 2662 1.44 - 1.57: 6174 1.57 - 1.69: 13 1.69 - 1.82: 78 Bond restraints: 10571 Sorted by residual: bond pdb=" C04 Q7G A1113 " pdb=" C05 Q7G A1113 " ideal model delta sigma weight residual 1.836 1.521 0.315 2.00e-02 2.50e+03 2.49e+02 bond pdb=" C04 Q7G B 403 " pdb=" C05 Q7G B 403 " ideal model delta sigma weight residual 1.836 1.523 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C04 Q7G B 404 " pdb=" C05 Q7G B 404 " ideal model delta sigma weight residual 1.836 1.526 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C04 Q7G A1112 " pdb=" C05 Q7G A1112 " ideal model delta sigma weight residual 1.836 1.532 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C13 Q7G B 404 " pdb=" C14 Q7G B 404 " ideal model delta sigma weight residual 1.599 1.316 0.283 2.00e-02 2.50e+03 2.00e+02 ... (remaining 10566 not shown) Histogram of bond angle deviations from ideal: 85.86 - 104.67: 212 104.67 - 123.49: 13873 123.49 - 142.30: 249 142.30 - 161.12: 0 161.12 - 179.93: 2 Bond angle restraints: 14336 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.10 -70.42 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" C5 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 111.64 86.42 25.22 3.00e+00 1.11e-01 7.06e+01 angle pdb=" C6 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 109.11 85.86 23.25 3.00e+00 1.11e-01 6.01e+01 angle pdb=" C7 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 108.24 86.95 21.29 3.00e+00 1.11e-01 5.04e+01 ... (remaining 14331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 6161 33.37 - 66.74: 335 66.74 - 100.11: 30 100.11 - 133.48: 19 133.48 - 166.85: 4 Dihedral angle restraints: 6549 sinusoidal: 2936 harmonic: 3613 Sorted by residual: dihedral pdb=" C2' ADP A1103 " pdb=" C1' ADP A1103 " pdb=" N9 ADP A1103 " pdb=" C4 ADP A1103 " ideal model delta sinusoidal sigma weight residual 91.55 -49.80 141.34 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O1B ADP A1103 " pdb=" O3A ADP A1103 " pdb=" PB ADP A1103 " pdb=" PA ADP A1103 " ideal model delta sinusoidal sigma weight residual 300.00 168.98 131.02 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" N PCW A1106 " pdb=" C4 PCW A1106 " pdb=" C5 PCW A1106 " pdb=" O4P PCW A1106 " ideal model delta sinusoidal sigma weight residual -66.66 100.19 -166.85 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 6546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 1616 0.172 - 0.345: 21 0.345 - 0.517: 1 0.517 - 0.689: 0 0.689 - 0.861: 4 Chirality restraints: 1642 Sorted by residual: chirality pdb=" C02 Q7G A1113 " pdb=" C03 Q7G A1113 " pdb=" C06 Q7G A1113 " pdb=" C10 Q7G A1113 " both_signs ideal model delta sigma weight residual False 2.14 3.00 -0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" C02 Q7G B 403 " pdb=" C03 Q7G B 403 " pdb=" C06 Q7G B 403 " pdb=" C10 Q7G B 403 " both_signs ideal model delta sigma weight residual False 2.14 2.99 -0.85 2.00e-01 2.50e+01 1.82e+01 chirality pdb=" C02 Q7G B 404 " pdb=" C03 Q7G B 404 " pdb=" C06 Q7G B 404 " pdb=" C10 Q7G B 404 " both_signs ideal model delta sigma weight residual False 2.14 2.99 -0.85 2.00e-01 2.50e+01 1.80e+01 ... (remaining 1639 not shown) Planarity restraints: 1753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G B 404 " 0.009 2.00e-02 2.50e+03 1.73e-01 3.73e+02 pdb=" C13 Q7G B 404 " 0.116 2.00e-02 2.50e+03 pdb=" C14 Q7G B 404 " 0.252 2.00e-02 2.50e+03 pdb=" C15 Q7G B 404 " -0.206 2.00e-02 2.50e+03 pdb=" C16 Q7G B 404 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.176 2.00e-02 2.50e+03 1.45e-01 2.65e+02 pdb=" C7 NAG B 401 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.236 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A1106 " 0.131 2.00e-02 2.50e+03 1.35e-01 1.83e+02 pdb=" C19 PCW A1106 " -0.117 2.00e-02 2.50e+03 pdb=" C20 PCW A1106 " -0.153 2.00e-02 2.50e+03 pdb=" C21 PCW A1106 " 0.139 2.00e-02 2.50e+03 ... (remaining 1750 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 4 2.13 - 2.82: 3093 2.82 - 3.51: 13662 3.51 - 4.21: 25660 4.21 - 4.90: 45360 Nonbonded interactions: 87779 Sorted by model distance: nonbonded pdb=" C4B Q7G A1113 " pdb=" O4 Q7G A1113 " model vdw 1.435 3.470 nonbonded pdb=" F3 ALF A1101 " pdb="MG MG A1102 " model vdw 1.836 2.120 nonbonded pdb=" OD1 ASP A 729 " pdb="MG MG A1102 " model vdw 1.975 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1102 " model vdw 2.088 2.170 nonbonded pdb=" F2 ALF A1101 " pdb=" O HOH A1201 " model vdw 2.162 2.390 ... (remaining 87774 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: 2.920 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: 15.570 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 34.910 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.015 0.315 10571 Z= 0.961 Angle : 1.325 70.417 14336 Z= 0.491 Chirality : 0.067 0.861 1642 Planarity : 0.008 0.173 1752 Dihedral : 20.576 166.853 4218 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.82 % Allowed : 20.39 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.58 (0.24), residues: 1242 helix: 1.20 (0.23), residues: 543 sheet: 0.20 (0.44), residues: 125 loop : -0.28 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.024 0.001 PHE A 128 TYR 0.014 0.001 TYR A 328 ARG 0.007 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 98 time to evaluate : 1.273 Fit side-chains REVERT: A 688 GLU cc_start: 0.7739 (mp0) cc_final: 0.7355 (mp0) outliers start: 41 outliers final: 36 residues processed: 138 average time/residue: 1.2373 time to fit residues: 184.3436 Evaluate side-chains 131 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 179 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 540 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN B 84 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10571 Z= 0.209 Angle : 0.624 9.180 14336 Z= 0.294 Chirality : 0.044 0.194 1642 Planarity : 0.005 0.050 1752 Dihedral : 17.925 177.723 1917 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.45 % Allowed : 19.65 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.35 (0.23), residues: 1242 helix: 0.83 (0.23), residues: 551 sheet: 0.31 (0.44), residues: 124 loop : -0.27 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.005 0.001 HIS A 245 PHE 0.013 0.001 PHE B 264 TYR 0.018 0.001 TYR B 39 ARG 0.005 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 101 time to evaluate : 1.110 Fit side-chains REVERT: A 480 MET cc_start: 0.7259 (mmm) cc_final: 0.6973 (mpm) REVERT: A 853 LYS cc_start: 0.7843 (mttt) cc_final: 0.7465 (mtmt) REVERT: B 177 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8622 (mm) outliers start: 37 outliers final: 24 residues processed: 132 average time/residue: 1.2786 time to fit residues: 181.3049 Evaluate side-chains 122 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 179 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 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: 0.8980 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10571 Z= 0.177 Angle : 0.570 7.148 14336 Z= 0.270 Chirality : 0.043 0.178 1642 Planarity : 0.005 0.053 1752 Dihedral : 16.293 177.594 1895 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.26 % Allowed : 20.30 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.37 (0.23), residues: 1242 helix: 0.81 (0.23), residues: 551 sheet: 0.34 (0.43), residues: 124 loop : -0.23 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.021 0.001 PHE A 128 TYR 0.013 0.001 TYR A 328 ARG 0.003 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 1.311 Fit side-chains REVERT: A 853 LYS cc_start: 0.7895 (mttt) cc_final: 0.7471 (mtmt) outliers start: 35 outliers final: 16 residues processed: 124 average time/residue: 1.3906 time to fit residues: 185.2404 Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10571 Z= 0.190 Angle : 0.564 7.673 14336 Z= 0.270 Chirality : 0.043 0.179 1642 Planarity : 0.005 0.051 1752 Dihedral : 15.551 176.230 1883 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.26 % Allowed : 19.93 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.35 (0.23), residues: 1242 helix: 0.80 (0.23), residues: 551 sheet: 0.40 (0.43), residues: 123 loop : -0.25 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.012 0.001 PHE B 264 TYR 0.013 0.001 TYR A 328 ARG 0.003 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 1.227 Fit side-chains REVERT: A 555 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7653 (mpp) outliers start: 35 outliers final: 21 residues processed: 122 average time/residue: 1.2875 time to fit residues: 169.5904 Evaluate side-chains 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 219 ASP 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: 2.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10571 Z= 0.228 Angle : 0.582 7.625 14336 Z= 0.281 Chirality : 0.044 0.184 1642 Planarity : 0.005 0.054 1752 Dihedral : 15.090 178.783 1881 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.35 % Allowed : 19.93 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.29 (0.23), residues: 1242 helix: 0.73 (0.23), residues: 551 sheet: 0.44 (0.43), residues: 123 loop : -0.29 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.006 0.001 HIS A 245 PHE 0.014 0.002 PHE A 583 TYR 0.015 0.002 TYR A 805 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 1.142 Fit side-chains REVERT: A 480 MET cc_start: 0.7393 (mpm) cc_final: 0.7132 (mmm) REVERT: A 555 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7775 (mpp) REVERT: A 671 GLU cc_start: 0.7572 (tp30) cc_final: 0.7193 (tp30) outliers start: 36 outliers final: 21 residues processed: 128 average time/residue: 1.2317 time to fit residues: 170.2580 Evaluate side-chains 118 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10571 Z= 0.170 Angle : 0.531 6.804 14336 Z= 0.259 Chirality : 0.043 0.176 1642 Planarity : 0.004 0.054 1752 Dihedral : 14.695 173.299 1881 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.61 % Allowed : 20.48 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.38 (0.23), residues: 1242 helix: 0.80 (0.23), residues: 551 sheet: 0.50 (0.44), residues: 123 loop : -0.25 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.003 0.001 HIS A 245 PHE 0.015 0.001 PHE A 128 TYR 0.012 0.001 TYR B 39 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.237 Fit side-chains REVERT: A 140 ASP cc_start: 0.7032 (m-30) cc_final: 0.6487 (m-30) REVERT: A 671 GLU cc_start: 0.7568 (tp30) cc_final: 0.7207 (tp30) outliers start: 28 outliers final: 21 residues processed: 115 average time/residue: 1.2648 time to fit residues: 156.7580 Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 219 ASP 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: 3.9990 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 119 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10571 Z= 0.141 Angle : 0.508 6.818 14336 Z= 0.248 Chirality : 0.042 0.170 1642 Planarity : 0.004 0.053 1752 Dihedral : 14.425 172.328 1881 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.61 % Allowed : 20.76 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.47 (0.24), residues: 1242 helix: 0.89 (0.23), residues: 552 sheet: 0.55 (0.44), residues: 123 loop : -0.21 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 968 HIS 0.005 0.001 HIS A 551 PHE 0.032 0.001 PHE A 128 TYR 0.011 0.001 TYR A 328 ARG 0.003 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.271 Fit side-chains REVERT: A 140 ASP cc_start: 0.7025 (m-30) cc_final: 0.6477 (m-30) REVERT: A 165 LYS cc_start: 0.7851 (mptp) cc_final: 0.6856 (mmtt) REVERT: A 221 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7237 (tt0) REVERT: A 671 GLU cc_start: 0.7503 (tp30) cc_final: 0.7108 (tp30) REVERT: A 688 GLU cc_start: 0.7741 (mp0) cc_final: 0.7366 (mp0) REVERT: B 249 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8515 (ptpt) outliers start: 28 outliers final: 21 residues processed: 116 average time/residue: 1.3404 time to fit residues: 167.6989 Evaluate side-chains 113 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 93 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10571 Z= 0.142 Angle : 0.507 6.860 14336 Z= 0.247 Chirality : 0.042 0.168 1642 Planarity : 0.004 0.052 1752 Dihedral : 14.246 171.390 1879 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.33 % Allowed : 20.76 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.52 (0.24), residues: 1242 helix: 0.93 (0.23), residues: 552 sheet: 0.63 (0.44), residues: 123 loop : -0.19 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.004 0.001 HIS A 551 PHE 0.022 0.001 PHE A 128 TYR 0.011 0.001 TYR A 328 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.202 Fit side-chains REVERT: A 165 LYS cc_start: 0.7841 (mptp) cc_final: 0.6856 (mmtt) REVERT: A 221 GLN cc_start: 0.7618 (tp-100) cc_final: 0.7226 (tt0) REVERT: A 246 GLU cc_start: 0.7450 (mp0) cc_final: 0.7211 (pm20) REVERT: A 671 GLU cc_start: 0.7497 (tp30) cc_final: 0.7115 (tp30) REVERT: B 249 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8500 (ptpt) outliers start: 25 outliers final: 20 residues processed: 116 average time/residue: 1.3415 time to fit residues: 167.2226 Evaluate side-chains 110 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.0970 chunk 104 optimal weight: 0.0980 chunk 111 optimal weight: 0.0040 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 0.0070 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 overall best weight: 0.1608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10571 Z= 0.116 Angle : 0.481 7.467 14336 Z= 0.234 Chirality : 0.041 0.161 1642 Planarity : 0.004 0.054 1752 Dihedral : 13.784 168.382 1879 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.49 % Allowed : 21.60 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.78 (0.24), residues: 1242 helix: 1.24 (0.24), residues: 538 sheet: 0.65 (0.44), residues: 124 loop : -0.12 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 32 HIS 0.010 0.001 HIS A 551 PHE 0.026 0.001 PHE A 128 TYR 0.009 0.001 TYR A 328 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.249 Fit side-chains REVERT: A 165 LYS cc_start: 0.7813 (mptp) cc_final: 0.6829 (mmtt) REVERT: A 216 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.5959 (tmm160) REVERT: A 221 GLN cc_start: 0.7574 (tp-100) cc_final: 0.7191 (tt0) REVERT: A 246 GLU cc_start: 0.7369 (mp0) cc_final: 0.7114 (pm20) REVERT: A 671 GLU cc_start: 0.7449 (tp30) cc_final: 0.7096 (tp30) REVERT: A 688 GLU cc_start: 0.7671 (mp0) cc_final: 0.7369 (mp0) REVERT: B 249 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8502 (ptpt) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 1.3433 time to fit residues: 178.7811 Evaluate side-chains 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 75 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10571 Z= 0.134 Angle : 0.506 9.240 14336 Z= 0.245 Chirality : 0.041 0.160 1642 Planarity : 0.004 0.052 1752 Dihedral : 13.708 167.398 1877 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.12 % Allowed : 23.00 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.82 (0.24), residues: 1242 helix: 1.20 (0.23), residues: 542 sheet: 0.72 (0.44), residues: 123 loop : -0.04 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 968 HIS 0.008 0.001 HIS A 551 PHE 0.026 0.001 PHE A 128 TYR 0.011 0.001 TYR A 328 ARG 0.002 0.000 ARG A 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.227 Fit side-chains REVERT: A 165 LYS cc_start: 0.7830 (mptp) cc_final: 0.6839 (mmtt) REVERT: A 216 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.5906 (tmm160) REVERT: A 221 GLN cc_start: 0.7585 (tp-100) cc_final: 0.7202 (tt0) REVERT: A 671 GLU cc_start: 0.7449 (tp30) cc_final: 0.7107 (tp30) REVERT: A 688 GLU cc_start: 0.7763 (mp0) cc_final: 0.7361 (mp0) REVERT: B 249 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8506 (ptpt) outliers start: 12 outliers final: 11 residues processed: 117 average time/residue: 1.3536 time to fit residues: 170.8333 Evaluate side-chains 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 249 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 12 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.151336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115936 restraints weight = 10602.250| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.47 r_work: 0.3203 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10571 Z= 0.160 Angle : 0.522 8.101 14336 Z= 0.255 Chirality : 0.042 0.162 1642 Planarity : 0.004 0.052 1752 Dihedral : 13.754 168.081 1877 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.68 % Allowed : 22.07 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.68 (0.24), residues: 1242 helix: 1.09 (0.23), residues: 545 sheet: 0.63 (0.44), residues: 124 loop : -0.10 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.009 0.001 HIS A 551 PHE 0.027 0.001 PHE A 128 TYR 0.012 0.001 TYR A 328 ARG 0.002 0.000 ARG A 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.11 seconds wall clock time: 71 minutes 6.55 seconds (4266.55 seconds total)