Starting phenix.real_space_refine on Thu Feb 15 00:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e21_30949/02_2024/7e21_30949.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e21_30949/02_2024/7e21_30949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e21_30949/02_2024/7e21_30949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e21_30949/02_2024/7e21_30949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e21_30949/02_2024/7e21_30949.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e21_30949/02_2024/7e21_30949.pdb" } resolution = 2.9 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= 0.006 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: 7 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 58 5.16 5 Na 4 4.78 5 C 6871 2.51 5 N 1720 2.21 5 O 1977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A GLU 1003": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7575 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 43, 'TRANS': 932} Chain breaks: 1 Chain: "B" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2404 Classifications: {'peptide': 294} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 273} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Unusual residues: {' MG': 1, ' NA': 4, 'AGS': 1, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'PC1': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 6.30, per 1000 atoms: 0.59 Number of scatterers: 10636 At special positions: 0 Unit cell: (89.134, 96.743, 181.529, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 5 15.00 Mg 1 11.99 Na 4 11.00 O 1977 8.00 N 1720 7.00 C 6871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 249 " distance=2.05 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 556 " distance=2.03 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=1.97 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 403 " - " ASN B 265 " " NAG D 1 " - " ASN B 158 " Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 42.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.957A pdb=" N ALA A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.651A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 122 removed outlier: 3.522A pdb=" N TRP A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 159 removed outlier: 3.791A pdb=" N GLY A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.056A pdb=" N ILE A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 311 removed outlier: 3.580A pdb=" N ILE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.657A pdb=" N VAL A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.761A pdb=" N THR A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.102A pdb=" N GLU A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 4.122A pdb=" N LEU A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 4.423A pdb=" N LEU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.625A pdb=" N GLY A 604 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 640 through 648 removed outlier: 3.938A pdb=" N ILE A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 680 removed outlier: 3.901A pdb=" N ASP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 removed outlier: 3.778A pdb=" N TYR A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 680 through 685' Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.644A pdb=" N ILE A 701 " --> pdb=" O GLN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 754 through 780 removed outlier: 3.977A pdb=" N ILE A 758 " --> pdb=" O ASN A 754 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP A 770 " --> pdb=" O ARG A 766 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 822 Proline residue: A 818 - end of helix removed outlier: 3.824A pdb=" N LEU A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.622A pdb=" N LYS A 833 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 834' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.824A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 removed outlier: 3.634A pdb=" N ILE A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 937 removed outlier: 3.624A pdb=" N ILE A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.883A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.525A pdb=" N LYS A1006 " --> pdb=" O ASP A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 removed outlier: 3.824A pdb=" N TYR A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 58 removed outlier: 3.519A pdb=" N PHE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.594A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.636A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.942A pdb=" N GLY B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.393A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 46 removed outlier: 3.690A pdb=" N GLY C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.934A pdb=" N CYS A 249 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 213 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU A 251 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 211 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 257 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE A 205 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 259 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU A 203 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.173A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 392 removed outlier: 3.579A pdb=" N THR A 387 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.542A pdb=" N PHE B 90 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 400 hydrogen bonds defined for protein. 1161 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: 3.18 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2206 1.33 - 1.47: 3741 1.47 - 1.62: 4789 1.62 - 1.76: 41 1.76 - 1.91: 85 Bond restraints: 10862 Sorted by residual: bond pdb=" C3' AGS A1106 " pdb=" C4' AGS A1106 " ideal model delta sigma weight residual 1.526 1.280 0.246 1.10e-02 8.26e+03 4.99e+02 bond pdb=" C1' AGS A1106 " pdb=" C2' AGS A1106 " ideal model delta sigma weight residual 1.530 1.307 0.223 1.30e-02 5.92e+03 2.94e+02 bond pdb=" C4 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 1.340 1.482 -0.142 1.00e-02 1.00e+04 2.01e+02 bond pdb=" C2 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 1.335 1.463 -0.128 1.00e-02 1.00e+04 1.63e+02 bond pdb=" C5 AGS A1106 " pdb=" C6 AGS A1106 " ideal model delta sigma weight residual 1.409 1.524 -0.115 1.00e-02 1.00e+04 1.33e+02 ... (remaining 10857 not shown) Histogram of bond angle deviations from ideal: 80.24 - 91.02: 3 91.02 - 101.79: 30 101.79 - 112.57: 5853 112.57 - 123.35: 8411 123.35 - 134.13: 443 Bond angle restraints: 14740 Sorted by residual: angle pdb=" N1 AGS A1106 " pdb=" C2 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 128.80 119.83 8.97 8.41e-01 1.41e+00 1.14e+02 angle pdb=" CAD Y01 A1107 " pdb=" CBH Y01 A1107 " pdb=" CBF Y01 A1107 " ideal model delta sigma weight residual 111.82 80.24 31.58 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C5 AGS A1106 " pdb=" N7 AGS A1106 " pdb=" C8 AGS A1106 " ideal model delta sigma weight residual 103.67 108.00 -4.33 4.26e-01 5.51e+00 1.03e+02 angle pdb=" C5 AGS A1106 " pdb=" C4 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 126.80 120.07 6.73 7.41e-01 1.82e+00 8.24e+01 angle pdb=" N7 AGS A1106 " pdb=" C8 AGS A1106 " pdb=" N9 AGS A1106 " ideal model delta sigma weight residual 114.03 108.06 5.97 6.99e-01 2.05e+00 7.29e+01 ... (remaining 14735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 6506 35.38 - 70.77: 226 70.77 - 106.15: 48 106.15 - 141.53: 110 141.53 - 176.91: 13 Dihedral angle restraints: 6903 sinusoidal: 3151 harmonic: 3752 Sorted by residual: dihedral pdb=" CB CYS A 518 " pdb=" SG CYS A 518 " pdb=" SG CYS A 556 " pdb=" CB CYS A 556 " ideal model delta sinusoidal sigma weight residual 93.00 23.32 69.68 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CA THR A 316 " pdb=" C THR A 316 " pdb=" N TRP A 317 " pdb=" CA TRP A 317 " ideal model delta harmonic sigma weight residual 180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA THR A 85 " pdb=" C THR A 85 " pdb=" N THR A 86 " pdb=" CA THR A 86 " ideal model delta harmonic sigma weight residual 180.00 152.34 27.66 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 6900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.195: 1636 1.195 - 2.390: 0 2.390 - 3.584: 0 3.584 - 4.779: 1 4.779 - 5.974: 29 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CBI Y01 A1107 " pdb=" CAU Y01 A1107 " pdb=" CBE Y01 A1107 " pdb=" CBG Y01 A1107 " both_signs ideal model delta sigma weight residual False 2.94 -3.04 5.97 2.00e-01 2.50e+01 8.92e+02 chirality pdb=" CBI Y01 C1501 " pdb=" CAU Y01 C1501 " pdb=" CBE Y01 C1501 " pdb=" CBG Y01 C1501 " both_signs ideal model delta sigma weight residual False 2.94 -3.04 5.97 2.00e-01 2.50e+01 8.92e+02 chirality pdb=" CBI Y01 A1110 " pdb=" CAU Y01 A1110 " pdb=" CBE Y01 A1110 " pdb=" CBG Y01 A1110 " both_signs ideal model delta sigma weight residual False 2.94 -3.03 5.97 2.00e-01 2.50e+01 8.90e+02 ... (remaining 1663 not shown) Planarity restraints: 1847 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 440 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO A 441 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 81 " 0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 82 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 132 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 133 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.040 5.00e-02 4.00e+02 ... (remaining 1844 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 161 2.64 - 3.21: 9054 3.21 - 3.77: 15621 3.77 - 4.34: 22126 4.34 - 4.90: 36703 Nonbonded interactions: 83665 Sorted by model distance: nonbonded pdb=" O TYR B 242 " pdb=" O TYR B 243 " model vdw 2.077 3.040 nonbonded pdb=" OD1 ASN A 174 " pdb=" N GLY A 175 " model vdw 2.119 2.520 nonbonded pdb=" NH1 ARG A 551 " pdb=" O1B AGS A1106 " model vdw 2.205 2.520 nonbonded pdb=" CAI Y01 A1109 " pdb=" CAD Y01 B 401 " model vdw 2.223 3.760 nonbonded pdb=" OE2 GLU A 875 " pdb=" OAG Y01 A1108 " model vdw 2.230 3.040 ... (remaining 83660 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: 0.540 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: 2.340 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.630 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.014 0.246 10862 Z= 0.932 Angle : 1.346 31.581 14740 Z= 0.656 Chirality : 0.724 5.974 1666 Planarity : 0.008 0.118 1845 Dihedral : 27.997 176.914 4478 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.81 % Favored : 91.34 % Rotamer: Outliers : 0.89 % Allowed : 6.70 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.81 (0.18), residues: 1294 helix: -2.62 (0.16), residues: 526 sheet: -1.12 (0.36), residues: 151 loop : -2.78 (0.21), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 890 HIS 0.006 0.001 HIS A 52 PHE 0.033 0.003 PHE A 793 TYR 0.045 0.003 TYR A 315 ARG 0.004 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.6382 (OUTLIER) cc_final: 0.6157 (p0) REVERT: A 261 THR cc_start: 0.8359 (p) cc_final: 0.8133 (t) REVERT: A 392 TRP cc_start: 0.8269 (t60) cc_final: 0.8028 (t60) REVERT: A 401 ASP cc_start: 0.7192 (t0) cc_final: 0.6755 (t0) REVERT: A 483 ASN cc_start: 0.7334 (p0) cc_final: 0.7062 (p0) REVERT: A 591 MET cc_start: 0.8884 (mtm) cc_final: 0.8648 (mpp) REVERT: A 649 ASN cc_start: 0.8379 (t0) cc_final: 0.8146 (t0) REVERT: A 729 ASP cc_start: 0.8676 (m-30) cc_final: 0.8442 (m-30) REVERT: A 764 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 22 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7481 (tttt) REVERT: C 42 LEU cc_start: 0.8146 (mt) cc_final: 0.7891 (mt) outliers start: 10 outliers final: 3 residues processed: 145 average time/residue: 1.2696 time to fit residues: 198.0787 Evaluate side-chains 89 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain B residue 159 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 436 ASN A 486 ASN A 582 ASN A 638 ASN A 649 ASN A 654 GLN A 697 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS B 18 ASN B 104 ASN B 140 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10862 Z= 0.203 Angle : 1.579 33.650 14740 Z= 0.583 Chirality : 0.154 1.916 1666 Planarity : 0.005 0.083 1845 Dihedral : 31.011 178.795 2014 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.03 % Favored : 92.66 % Rotamer: Outliers : 2.77 % Allowed : 10.99 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1294 helix: -0.73 (0.22), residues: 539 sheet: -1.00 (0.37), residues: 153 loop : -2.42 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 931 HIS 0.004 0.001 HIS A 493 PHE 0.026 0.002 PHE A 870 TYR 0.019 0.001 TYR C 21 ARG 0.009 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 315 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6876 (m-10) REVERT: A 362 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: A 392 TRP cc_start: 0.8302 (t60) cc_final: 0.8063 (t60) REVERT: A 401 ASP cc_start: 0.7020 (t0) cc_final: 0.6613 (t0) REVERT: A 483 ASN cc_start: 0.7450 (p0) cc_final: 0.6956 (p0) REVERT: A 591 MET cc_start: 0.8772 (mtm) cc_final: 0.8504 (mpp) REVERT: A 649 ASN cc_start: 0.8401 (t0) cc_final: 0.7696 (t0) REVERT: A 729 ASP cc_start: 0.8706 (m-30) cc_final: 0.8479 (m-30) REVERT: A 764 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 1019 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8326 (mtpt) REVERT: B 22 LYS cc_start: 0.7937 (mtmm) cc_final: 0.7528 (tttt) REVERT: B 203 LYS cc_start: 0.7682 (tptp) cc_final: 0.7264 (mtpt) REVERT: C 42 LEU cc_start: 0.7822 (mt) cc_final: 0.7566 (mt) outliers start: 31 outliers final: 5 residues processed: 119 average time/residue: 1.1240 time to fit residues: 145.8562 Evaluate side-chains 91 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 1019 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.0010 chunk 97 optimal weight: 0.9990 chunk 79 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 436 ASN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10862 Z= 0.214 Angle : 1.553 33.203 14740 Z= 0.569 Chirality : 0.149 1.914 1666 Planarity : 0.004 0.067 1845 Dihedral : 30.784 179.986 2009 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.80 % Favored : 92.89 % Rotamer: Outliers : 2.41 % Allowed : 12.96 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.48 (0.23), residues: 1294 helix: 0.21 (0.23), residues: 531 sheet: -0.61 (0.39), residues: 144 loop : -2.21 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 PHE 0.018 0.001 PHE A 870 TYR 0.025 0.002 TYR A 488 ARG 0.011 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 315 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6782 (m-10) REVERT: A 401 ASP cc_start: 0.7017 (t0) cc_final: 0.6491 (t0) REVERT: A 483 ASN cc_start: 0.7306 (p0) cc_final: 0.6799 (p0) REVERT: A 649 ASN cc_start: 0.8408 (t0) cc_final: 0.7717 (t0) REVERT: A 764 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 22 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7570 (tttt) REVERT: B 203 LYS cc_start: 0.7574 (tptp) cc_final: 0.7200 (mmmt) outliers start: 27 outliers final: 10 residues processed: 110 average time/residue: 1.1239 time to fit residues: 135.0918 Evaluate side-chains 91 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 30.0000 chunk 12 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 436 ASN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10862 Z= 0.186 Angle : 1.536 33.290 14740 Z= 0.559 Chirality : 0.149 1.890 1666 Planarity : 0.004 0.060 1845 Dihedral : 30.635 179.862 2009 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.03 % Favored : 92.74 % Rotamer: Outliers : 3.04 % Allowed : 14.30 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.09 (0.23), residues: 1294 helix: 0.60 (0.24), residues: 536 sheet: -0.73 (0.41), residues: 138 loop : -1.97 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 PHE 0.014 0.001 PHE A 870 TYR 0.028 0.001 TYR A 488 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 86 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 183 GLU cc_start: 0.8239 (pt0) cc_final: 0.7991 (pm20) REVERT: A 483 ASN cc_start: 0.7219 (p0) cc_final: 0.6651 (p0) REVERT: A 544 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 649 ASN cc_start: 0.8388 (t0) cc_final: 0.7723 (t0) REVERT: A 764 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 22 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7574 (tttt) REVERT: B 203 LYS cc_start: 0.7536 (tptp) cc_final: 0.7186 (mmmt) outliers start: 34 outliers final: 16 residues processed: 113 average time/residue: 1.1006 time to fit residues: 135.4733 Evaluate side-chains 98 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10862 Z= 0.211 Angle : 1.540 33.519 14740 Z= 0.561 Chirality : 0.149 1.893 1666 Planarity : 0.004 0.056 1845 Dihedral : 30.588 179.968 2009 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.26 % Favored : 92.50 % Rotamer: Outliers : 2.86 % Allowed : 15.73 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.90 (0.23), residues: 1294 helix: 0.82 (0.24), residues: 530 sheet: -0.60 (0.41), residues: 134 loop : -1.90 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 317 HIS 0.002 0.001 HIS A 882 PHE 0.016 0.001 PHE A 793 TYR 0.028 0.001 TYR A 488 ARG 0.003 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 81 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: A 183 GLU cc_start: 0.8251 (pt0) cc_final: 0.7990 (pm20) REVERT: A 324 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8428 (tp) REVERT: A 483 ASN cc_start: 0.7151 (p0) cc_final: 0.6576 (p0) REVERT: A 544 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 649 ASN cc_start: 0.8383 (t0) cc_final: 0.7724 (t0) REVERT: A 764 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 22 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7347 (tttt) REVERT: B 203 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7166 (mmmt) REVERT: B 268 MET cc_start: 0.7498 (mmt) cc_final: 0.7099 (mmt) outliers start: 32 outliers final: 17 residues processed: 106 average time/residue: 1.1665 time to fit residues: 134.6811 Evaluate side-chains 101 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 434 GLN A 436 ASN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10862 Z= 0.177 Angle : 1.530 33.247 14740 Z= 0.554 Chirality : 0.150 1.884 1666 Planarity : 0.004 0.054 1845 Dihedral : 30.410 179.998 2009 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.26 % Favored : 92.58 % Rotamer: Outliers : 2.50 % Allowed : 15.82 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.70 (0.24), residues: 1294 helix: 1.01 (0.24), residues: 532 sheet: -0.66 (0.41), residues: 138 loop : -1.78 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.002 0.000 HIS A 493 PHE 0.013 0.001 PHE A 793 TYR 0.019 0.001 TYR B 204 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7518 (tm) cc_final: 0.7094 (mm) REVERT: A 178 MET cc_start: 0.7928 (ptp) cc_final: 0.7507 (ptp) REVERT: A 483 ASN cc_start: 0.7201 (p0) cc_final: 0.6633 (p0) REVERT: A 544 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 649 ASN cc_start: 0.8442 (t0) cc_final: 0.7766 (t0) REVERT: A 764 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 22 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7361 (tttp) REVERT: B 203 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7134 (mmmt) outliers start: 28 outliers final: 14 residues processed: 113 average time/residue: 1.2315 time to fit residues: 151.7173 Evaluate side-chains 99 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 69 optimal weight: 0.0670 chunk 124 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 10862 Z= 0.153 Angle : 1.513 32.696 14740 Z= 0.546 Chirality : 0.151 1.929 1666 Planarity : 0.004 0.051 1845 Dihedral : 30.253 179.659 2007 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.96 % Favored : 92.89 % Rotamer: Outliers : 1.52 % Allowed : 17.25 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.44 (0.24), residues: 1294 helix: 1.17 (0.24), residues: 534 sheet: -0.42 (0.41), residues: 148 loop : -1.64 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 PHE 0.015 0.001 PHE A 578 TYR 0.031 0.001 TYR A 488 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 118 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: A 289 GLU cc_start: 0.7885 (pt0) cc_final: 0.7672 (tt0) REVERT: A 483 ASN cc_start: 0.7207 (p0) cc_final: 0.6607 (p0) REVERT: A 544 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: A 649 ASN cc_start: 0.8445 (t0) cc_final: 0.7789 (t0) REVERT: A 764 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 22 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7571 (tttt) REVERT: B 203 LYS cc_start: 0.7495 (tptp) cc_final: 0.7198 (mmmt) outliers start: 17 outliers final: 8 residues processed: 110 average time/residue: 1.1385 time to fit residues: 136.8161 Evaluate side-chains 93 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 9.9990 chunk 74 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10862 Z= 0.190 Angle : 1.521 32.971 14740 Z= 0.551 Chirality : 0.151 1.895 1666 Planarity : 0.004 0.056 1845 Dihedral : 30.169 179.558 2007 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.80 % Favored : 93.04 % Rotamer: Outliers : 1.97 % Allowed : 17.61 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.36 (0.24), residues: 1294 helix: 1.28 (0.24), residues: 528 sheet: -0.51 (0.39), residues: 158 loop : -1.57 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 317 HIS 0.004 0.001 HIS A 493 PHE 0.014 0.001 PHE A 793 TYR 0.021 0.001 TYR B 204 ARG 0.002 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 118 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: A 178 MET cc_start: 0.8032 (ptp) cc_final: 0.7632 (ptp) REVERT: A 483 ASN cc_start: 0.7266 (p0) cc_final: 0.6672 (p0) REVERT: A 544 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 649 ASN cc_start: 0.8427 (t0) cc_final: 0.7741 (t0) REVERT: A 764 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 22 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7375 (tttp) REVERT: B 203 LYS cc_start: 0.7474 (tptp) cc_final: 0.7141 (mmmt) outliers start: 22 outliers final: 12 residues processed: 101 average time/residue: 1.1527 time to fit residues: 127.1133 Evaluate side-chains 96 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10862 Z= 0.236 Angle : 1.534 33.277 14740 Z= 0.560 Chirality : 0.151 1.888 1666 Planarity : 0.004 0.051 1845 Dihedral : 30.154 178.300 2007 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.50 % Favored : 92.35 % Rotamer: Outliers : 1.61 % Allowed : 17.78 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.43 (0.24), residues: 1294 helix: 1.31 (0.24), residues: 522 sheet: -0.52 (0.40), residues: 144 loop : -1.67 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 894 HIS 0.003 0.001 HIS A 493 PHE 0.017 0.001 PHE A 793 TYR 0.030 0.002 TYR A 488 ARG 0.002 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7921 (ptp) cc_final: 0.7541 (ptp) REVERT: A 483 ASN cc_start: 0.7234 (p0) cc_final: 0.6625 (p0) REVERT: A 649 ASN cc_start: 0.8417 (t0) cc_final: 0.7746 (t0) REVERT: A 764 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 22 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7560 (tttt) REVERT: B 203 LYS cc_start: 0.7459 (tptp) cc_final: 0.7218 (mtmp) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 1.2395 time to fit residues: 125.3611 Evaluate side-chains 91 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10862 Z= 0.207 Angle : 1.529 33.102 14740 Z= 0.558 Chirality : 0.151 1.886 1666 Planarity : 0.004 0.049 1845 Dihedral : 30.139 178.198 2007 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.42 % Favored : 92.43 % Rotamer: Outliers : 1.70 % Allowed : 17.78 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.40 (0.24), residues: 1294 helix: 1.28 (0.24), residues: 528 sheet: -0.56 (0.40), residues: 148 loop : -1.61 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 PHE 0.015 0.001 PHE A 793 TYR 0.022 0.001 TYR B 204 ARG 0.001 0.000 ARG B 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 118 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: A 178 MET cc_start: 0.7896 (ptp) cc_final: 0.7374 (ptp) REVERT: A 483 ASN cc_start: 0.7370 (p0) cc_final: 0.6792 (p0) REVERT: A 544 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: A 649 ASN cc_start: 0.8426 (t0) cc_final: 0.7764 (t0) REVERT: A 764 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 22 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7575 (tttt) REVERT: B 23 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7328 (mt-10) REVERT: B 203 LYS cc_start: 0.7505 (tptp) cc_final: 0.7196 (mtmp) outliers start: 19 outliers final: 14 residues processed: 92 average time/residue: 1.3546 time to fit residues: 135.6484 Evaluate side-chains 93 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093594 restraints weight = 17237.900| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.14 r_work: 0.3080 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10862 Z= 0.167 Angle : 1.515 32.622 14740 Z= 0.549 Chirality : 0.152 1.894 1666 Planarity : 0.004 0.044 1845 Dihedral : 30.092 178.985 2007 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.80 % Favored : 93.04 % Rotamer: Outliers : 1.34 % Allowed : 18.23 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.27 (0.24), residues: 1294 helix: 1.35 (0.24), residues: 530 sheet: -0.41 (0.41), residues: 148 loop : -1.53 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.004 0.000 HIS A 493 PHE 0.017 0.001 PHE A 578 TYR 0.031 0.001 TYR A 488 ARG 0.004 0.000 ARG A 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.35 seconds wall clock time: 63 minutes 37.45 seconds (3817.45 seconds total)