Starting phenix.real_space_refine on Sat Dec 9 08:55:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2023/6k7g_9931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2023/6k7g_9931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2023/6k7g_9931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2023/6k7g_9931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2023/6k7g_9931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2023/6k7g_9931.pdb" } resolution = 3.3 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= 0.004 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6852 2.51 5 N 1747 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A ASP 816": "OD1" <-> "OD2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1022": "OD1" <-> "OD2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10569 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7852 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 957} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.22, per 1000 atoms: 0.59 Number of scatterers: 10569 At special positions: 0 Unit cell: (66.4, 111.22, 164.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1914 8.00 N 1747 7.00 C 6852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.02 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 47.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 132 removed outlier: 4.257A pdb=" N LYS A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.016A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.681A pdb=" N HIS A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.935A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 619 through 633 removed outlier: 4.505A pdb=" N LEU A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 787 through 797 removed outlier: 4.390A pdb=" N SER A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET A 793 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 831 Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 856 through 861 removed outlier: 3.746A pdb=" N TRP A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.155A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.717A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.086A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1013 removed outlier: 3.611A pdb=" N HIS A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A1004 " --> pdb=" O ILE A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1034 through 1061 removed outlier: 3.747A pdb=" N MET A1038 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.992A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 74 Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.605A pdb=" N ARG C 161 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.511A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 4.076A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 323 through 350 removed outlier: 3.884A pdb=" N HIS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.709A pdb=" N VAL A 146 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 160 removed outlier: 3.971A pdb=" N ASP A 155 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 198 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.633A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 425 removed outlier: 6.499A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS A 647 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 553 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.510A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.764A pdb=" N MET C 120 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG C 274 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.205A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.568A pdb=" N GLY C 289 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 186 " --> pdb=" O SER C 292 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1350 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: 3.62 Time building geometry restraints manager: 4.62 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: 1899 1.32 - 1.45: 2821 1.45 - 1.57: 6013 1.57 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 10818 Sorted by residual: bond pdb=" C SER A 223 " pdb=" N PRO A 224 " ideal model delta sigma weight residual 1.330 1.370 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" C VAL C 99 " pdb=" N THR C 100 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 9.10e+00 bond pdb=" C1 MAN B 3 " pdb=" O5 MAN B 3 " ideal model delta sigma weight residual 1.399 1.453 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" CG GLN A 870 " pdb=" CD GLN A 870 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.04e+00 bond pdb=" CB VAL A 853 " pdb=" CG2 VAL A 853 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.61e+00 ... (remaining 10813 not shown) Histogram of bond angle deviations from ideal: 93.63 - 102.33: 41 102.33 - 111.04: 3910 111.04 - 119.74: 5689 119.74 - 128.45: 4948 128.45 - 137.15: 101 Bond angle restraints: 14689 Sorted by residual: angle pdb=" C HIS A 227 " pdb=" N LEU A 228 " pdb=" CA LEU A 228 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C GLU A 633 " pdb=" N LYS A 634 " pdb=" CA LYS A 634 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C ILE A 803 " pdb=" N SER A 804 " pdb=" CA SER A 804 " ideal model delta sigma weight residual 121.19 128.16 -6.97 1.59e+00 3.96e-01 1.92e+01 angle pdb=" N GLU C 158 " pdb=" CA GLU C 158 " pdb=" C GLU C 158 " ideal model delta sigma weight residual 109.81 119.38 -9.57 2.21e+00 2.05e-01 1.88e+01 angle pdb=" C THR A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta sigma weight residual 127.00 137.15 -10.15 2.40e+00 1.74e-01 1.79e+01 ... (remaining 14684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5738 17.70 - 35.40: 628 35.40 - 53.10: 127 53.10 - 70.80: 25 70.80 - 88.50: 12 Dihedral angle restraints: 6530 sinusoidal: 2698 harmonic: 3832 Sorted by residual: dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.87 -62.87 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA ALA C 169 " pdb=" C ALA C 169 " pdb=" N PRO C 170 " pdb=" CA PRO C 170 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU C 111 " pdb=" C GLU C 111 " pdb=" N LYS C 112 " pdb=" CA LYS C 112 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 6527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1272 0.074 - 0.147: 361 0.147 - 0.221: 40 0.221 - 0.295: 8 0.295 - 0.369: 2 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CB VAL A 103 " pdb=" CA VAL A 103 " pdb=" CG1 VAL A 103 " pdb=" CG2 VAL A 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1680 not shown) Planarity restraints: 1839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.323 2.00e-02 2.50e+03 2.81e-01 9.89e+02 pdb=" C7 NAG B 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.052 2.00e-02 2.50e+03 4.27e-02 2.28e+01 pdb=" C7 NAG C 401 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.067 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 255 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU C 255 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU C 255 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP C 256 " 0.023 2.00e-02 2.50e+03 ... (remaining 1836 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2616 2.79 - 3.32: 9540 3.32 - 3.84: 17816 3.84 - 4.37: 20955 4.37 - 4.90: 36245 Nonbonded interactions: 87172 Sorted by model distance: nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.262 2.440 nonbonded pdb=" OG SER A 94 " pdb=" O GLY A 97 " model vdw 2.275 2.440 nonbonded pdb=" O MET A1038 " pdb=" OH TYR C 329 " model vdw 2.313 2.440 nonbonded pdb=" NE2 GLN A 795 " pdb=" OG SER A 814 " model vdw 2.314 2.520 nonbonded pdb=" OH TYR A 611 " pdb=" OE1 GLU A 626 " model vdw 2.329 2.440 ... (remaining 87167 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.240 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 32.100 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.012 0.108 10818 Z= 0.787 Angle : 1.183 13.907 14689 Z= 0.624 Chirality : 0.068 0.369 1683 Planarity : 0.011 0.281 1836 Dihedral : 15.509 88.497 4049 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.13 % Favored : 90.71 % Rotamer: Outliers : 0.43 % Allowed : 9.39 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -4.12 (0.18), residues: 1303 helix: -2.64 (0.15), residues: 589 sheet: -1.36 (0.37), residues: 171 loop : -3.20 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 927 HIS 0.020 0.003 HIS A 936 PHE 0.037 0.003 PHE C 304 TYR 0.036 0.004 TYR C 122 ARG 0.008 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 129 average time/residue: 0.3395 time to fit residues: 56.7577 Evaluate side-chains 88 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1032 time to fit residues: 2.2332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 147 HIS A 187 ASN A 264 HIS ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 451 ASN A 456 HIS A 530 ASN A 679 ASN A 993 HIS C 92 ASN C 131 HIS C 254 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10818 Z= 0.190 Angle : 0.653 11.069 14689 Z= 0.334 Chirality : 0.044 0.187 1683 Planarity : 0.005 0.059 1836 Dihedral : 6.761 58.815 1570 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.48 % Allowed : 12.00 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -2.43 (0.21), residues: 1303 helix: -0.78 (0.20), residues: 572 sheet: -1.23 (0.37), residues: 175 loop : -2.62 (0.23), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 262 HIS 0.008 0.001 HIS A 264 PHE 0.018 0.001 PHE A 968 TYR 0.017 0.001 TYR C 82 ARG 0.004 0.000 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 117 average time/residue: 0.2650 time to fit residues: 44.0438 Evaluate side-chains 101 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1047 time to fit residues: 3.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 GLN C 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10818 Z= 0.280 Angle : 0.669 11.496 14689 Z= 0.339 Chirality : 0.045 0.166 1683 Planarity : 0.005 0.059 1836 Dihedral : 6.481 59.896 1570 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.06 % Favored : 91.86 % Rotamer: Outliers : 1.22 % Allowed : 15.13 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.81 (0.22), residues: 1303 helix: -0.19 (0.21), residues: 576 sheet: -0.93 (0.39), residues: 170 loop : -2.37 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 927 HIS 0.010 0.002 HIS A 473 PHE 0.021 0.002 PHE C 304 TYR 0.021 0.002 TYR C 122 ARG 0.004 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.2634 time to fit residues: 39.9894 Evaluate side-chains 97 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1017 time to fit residues: 3.1907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 125 optimal weight: 0.5980 chunk 62 optimal weight: 0.0970 chunk 112 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10818 Z= 0.156 Angle : 0.589 11.816 14689 Z= 0.299 Chirality : 0.043 0.174 1683 Planarity : 0.004 0.056 1836 Dihedral : 6.084 59.870 1570 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.39 % Allowed : 15.57 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1303 helix: 0.32 (0.22), residues: 578 sheet: -0.89 (0.39), residues: 178 loop : -2.16 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 262 HIS 0.003 0.001 HIS A 264 PHE 0.018 0.001 PHE A 594 TYR 0.011 0.001 TYR C 273 ARG 0.014 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 113 average time/residue: 0.2565 time to fit residues: 41.2098 Evaluate side-chains 102 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1068 time to fit residues: 3.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.0040 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10818 Z= 0.244 Angle : 0.620 11.947 14689 Z= 0.313 Chirality : 0.044 0.151 1683 Planarity : 0.004 0.056 1836 Dihedral : 6.033 59.805 1570 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.48 % Rotamer: Outliers : 0.87 % Allowed : 17.39 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.15 (0.23), residues: 1303 helix: 0.38 (0.22), residues: 579 sheet: -0.71 (0.39), residues: 176 loop : -2.04 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.010 0.001 HIS A 473 PHE 0.018 0.002 PHE C 304 TYR 0.019 0.001 TYR C 122 ARG 0.009 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 102 average time/residue: 0.2692 time to fit residues: 38.5934 Evaluate side-chains 94 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1003 time to fit residues: 2.2567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.0030 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10818 Z= 0.143 Angle : 0.571 12.939 14689 Z= 0.288 Chirality : 0.042 0.147 1683 Planarity : 0.004 0.055 1836 Dihedral : 5.744 59.683 1570 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.70 % Allowed : 18.17 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.84 (0.24), residues: 1303 helix: 0.70 (0.22), residues: 576 sheet: -0.57 (0.40), residues: 175 loop : -1.93 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 262 HIS 0.005 0.001 HIS A 264 PHE 0.018 0.001 PHE A 594 TYR 0.012 0.001 TYR A 70 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 107 average time/residue: 0.2340 time to fit residues: 36.4535 Evaluate side-chains 98 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1088 time to fit residues: 2.7466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 795 GLN C 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10818 Z= 0.163 Angle : 0.591 12.604 14689 Z= 0.295 Chirality : 0.042 0.149 1683 Planarity : 0.004 0.053 1836 Dihedral : 5.640 59.865 1570 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.43 % Allowed : 18.35 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.81 (0.24), residues: 1303 helix: 0.73 (0.22), residues: 580 sheet: -0.42 (0.40), residues: 175 loop : -1.99 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 262 HIS 0.004 0.001 HIS A 323 PHE 0.034 0.001 PHE A 594 TYR 0.013 0.001 TYR C 122 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 99 average time/residue: 0.2498 time to fit residues: 35.5558 Evaluate side-chains 93 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1031 time to fit residues: 2.0229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN C 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10818 Z= 0.240 Angle : 0.610 12.984 14689 Z= 0.307 Chirality : 0.043 0.158 1683 Planarity : 0.004 0.053 1836 Dihedral : 5.767 59.991 1570 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.78 % Allowed : 18.26 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1303 helix: 0.64 (0.22), residues: 584 sheet: -0.21 (0.43), residues: 162 loop : -1.97 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.006 0.001 HIS A 323 PHE 0.020 0.002 PHE A 594 TYR 0.019 0.001 TYR C 122 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 99 average time/residue: 0.2404 time to fit residues: 34.9434 Evaluate side-chains 94 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1021 time to fit residues: 2.3516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN A 264 HIS C 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10818 Z= 0.207 Angle : 0.602 13.717 14689 Z= 0.303 Chirality : 0.043 0.156 1683 Planarity : 0.004 0.053 1836 Dihedral : 5.742 59.907 1570 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.26 % Allowed : 18.43 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.79 (0.24), residues: 1303 helix: 0.64 (0.22), residues: 582 sheet: -0.19 (0.42), residues: 166 loop : -1.93 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.011 0.001 HIS A 473 PHE 0.024 0.002 PHE A 594 TYR 0.016 0.001 TYR C 122 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.2611 time to fit residues: 37.2650 Evaluate side-chains 93 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1002 time to fit residues: 1.9864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10818 Z= 0.262 Angle : 0.635 14.130 14689 Z= 0.319 Chirality : 0.044 0.158 1683 Planarity : 0.004 0.052 1836 Dihedral : 5.842 59.859 1570 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 19.57 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1303 helix: 0.60 (0.22), residues: 583 sheet: -0.14 (0.42), residues: 166 loop : -1.95 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.011 0.001 HIS A 473 PHE 0.025 0.002 PHE A 594 TYR 0.020 0.001 TYR C 122 ARG 0.005 0.000 ARG A 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2663 time to fit residues: 35.7131 Evaluate side-chains 92 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.181652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135650 restraints weight = 11178.343| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.36 r_work: 0.3153 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10818 Z= 0.270 Angle : 0.623 13.559 14689 Z= 0.315 Chirality : 0.044 0.160 1683 Planarity : 0.004 0.054 1836 Dihedral : 5.927 59.888 1570 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.52 % Allowed : 19.13 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.83 (0.24), residues: 1303 helix: 0.56 (0.22), residues: 582 sheet: -0.16 (0.43), residues: 162 loop : -1.90 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.018 0.002 HIS A 264 PHE 0.021 0.002 PHE A 594 TYR 0.025 0.002 TYR A 486 ARG 0.004 0.000 ARG A 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.66 seconds wall clock time: 41 minutes 50.86 seconds (2510.86 seconds total)