Starting phenix.real_space_refine on Sat Dec 9 08:41:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2023/6k7n_9942.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2023/6k7n_9942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2023/6k7n_9942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2023/6k7n_9942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2023/6k7n_9942.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7n_9942/12_2023/6k7n_9942.pdb" } resolution = 2.84 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= 0.005 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 Al 1 5.89 5 Mg 1 5.21 5 S 56 5.16 5 C 6834 2.51 5 N 1745 2.21 5 O 1903 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "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 TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 771": "OE1" <-> "OE2" 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 ARG 875": "NH1" <-> "NH2" 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 ASP 920": "OD1" <-> "OD2" 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 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 PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "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 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10544 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7821 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 952} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 3, 'PTRANS': 22, '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: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' MG': 1, 'ALF': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" 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 Time building chain proxies: 6.36, per 1000 atoms: 0.60 Number of scatterers: 10544 At special positions: 0 Unit cell: (68.89, 109.56, 165.17, 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 56 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1903 8.00 N 1745 7.00 C 6834 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=2.02 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=2.04 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: 4.53 Conformation dependent library (CDL) restraints added in 2.1 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 48.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 131 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 210 through 215 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.616A pdb=" N ASP A 273 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 288 through 324 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: 4.119A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.533A 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 447 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.787A pdb=" N PHE A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 570 through 588 removed outlier: 5.569A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 617 removed outlier: 4.154A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 685 removed outlier: 4.588A pdb=" N ASN A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 751 removed outlier: 3.925A pdb=" N LEU A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 787 through 797 removed outlier: 4.622A pdb=" N SER A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 5.153A 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 823 through 831 removed outlier: 4.252A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 856 Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.657A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'A' and resid 887 through 896 removed outlier: 3.993A 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 919 removed outlier: 3.615A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (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: 3.832A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.577A pdb=" N SER A1024 " --> pdb=" O PRO A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1033 through 1062 removed outlier: 3.655A pdb=" N TRP A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.155A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A1062 " --> pdb=" O LYS A1058 " (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 146 through 152 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: 3.530A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 removed outlier: 3.964A pdb=" N ILE C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.985A pdb=" N VAL A 263 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 7.785A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 782 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 406 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A 784 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER A 408 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 759 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 729 " --> pdb=" O CYS A 759 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 728 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 425 removed outlier: 7.201A pdb=" N MET A 419 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS A 647 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE A 421 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU A 645 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 423 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 641 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA7, first strand: chain 'A' and resid 545 through 547 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.944A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.301A 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 110 removed outlier: 4.343A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 295 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 162 through 163 removed outlier: 3.573A pdb=" N LYS C 166 " --> pdb=" O ASN C 163 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1368 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: 3.68 Time building geometry restraints manager: 4.75 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: 1846 1.32 - 1.44: 2834 1.44 - 1.57: 6020 1.57 - 1.69: 1 1.69 - 1.82: 89 Bond restraints: 10790 Sorted by residual: bond pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.684 1.791 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F4 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.686 1.793 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.790 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C ILE C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.09e+01 ... (remaining 10785 not shown) Histogram of bond angle deviations from ideal: 88.85 - 107.03: 369 107.03 - 125.20: 14044 125.20 - 143.38: 234 143.38 - 161.55: 0 161.55 - 179.73: 2 Bond angle restraints: 14649 Sorted by residual: angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F2 ALF A1301 " ideal model delta sigma weight residual 108.68 179.73 -71.05 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.63 177.39 -67.76 3.00e+00 1.11e-01 5.10e+02 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 110.21 88.85 21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.69 89.52 20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.59 90.70 18.89 3.00e+00 1.11e-01 3.96e+01 ... (remaining 14644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.56: 5913 20.56 - 41.12: 513 41.12 - 61.68: 66 61.68 - 82.24: 10 82.24 - 102.80: 13 Dihedral angle restraints: 6515 sinusoidal: 2698 harmonic: 3817 Sorted by residual: dihedral pdb=" CA ARG A 479 " pdb=" C ARG A 479 " pdb=" N GLU A 480 " pdb=" CA GLU A 480 " ideal model delta harmonic sigma weight residual 180.00 146.31 33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA THR A 535 " pdb=" C THR A 535 " pdb=" N SER A 536 " pdb=" CA SER A 536 " ideal model delta harmonic sigma weight residual -180.00 -146.87 -33.13 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 0.00 32.24 -32.24 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1380 0.094 - 0.187: 276 0.187 - 0.281: 20 0.281 - 0.375: 1 0.375 - 0.468: 1 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CB ILE A 694 " pdb=" CA ILE A 694 " pdb=" CG1 ILE A 694 " pdb=" CG2 ILE A 694 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CG LEU A 854 " pdb=" CB LEU A 854 " pdb=" CD1 LEU A 854 " pdb=" CD2 LEU A 854 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+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 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1675 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.40e+02 pdb=" C7 NAG C 402 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.391 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.220 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG C 401 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.058 2.00e-02 2.50e+03 5.08e-02 3.22e+01 pdb=" C7 NAG B 1 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.047 2.00e-02 2.50e+03 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 111 2.62 - 3.19: 8625 3.19 - 3.76: 17111 3.76 - 4.33: 24221 4.33 - 4.90: 38949 Nonbonded interactions: 89017 Sorted by model distance: nonbonded pdb=" F3 ALF A1301 " pdb="MG MG A1303 " model vdw 2.046 2.120 nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1303 " model vdw 2.233 2.170 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.243 2.440 nonbonded pdb=" OG SER A 767 " pdb=" OG SER A 792 " model vdw 2.293 2.440 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.297 2.440 ... (remaining 89012 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: 1.680 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.290 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 33.080 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.013 0.107 10790 Z= 0.824 Angle : 1.533 71.046 14649 Z= 0.733 Chirality : 0.072 0.468 1678 Planarity : 0.011 0.226 1828 Dihedral : 15.821 102.800 4044 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.01 % Favored : 91.91 % Rotamer: Outliers : 0.44 % Allowed : 8.54 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % 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: -3.74 (0.19), residues: 1298 helix: -2.16 (0.16), residues: 560 sheet: -1.53 (0.39), residues: 144 loop : -3.03 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 143 HIS 0.024 0.003 HIS C 302 PHE 0.031 0.004 PHE C 179 TYR 0.031 0.004 TYR C 297 ARG 0.012 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.373 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 1.3813 time to fit residues: 182.8360 Evaluate side-chains 89 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.3152 time to fit residues: 3.0976 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 227 HIS A 234 ASN A 433 GLN A 454 ASN A 605 GLN A 612 GLN A 682 HIS A 765 GLN A 967 ASN C 92 ASN C 176 ASN C 222 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10790 Z= 0.217 Angle : 0.713 9.986 14649 Z= 0.367 Chirality : 0.046 0.187 1678 Planarity : 0.006 0.067 1828 Dihedral : 9.040 78.600 1566 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.24 % Favored : 93.61 % Rotamer: Outliers : 2.79 % Allowed : 13.34 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -2.31 (0.21), residues: 1298 helix: -0.63 (0.20), residues: 572 sheet: -1.22 (0.39), residues: 153 loop : -2.57 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 876 HIS 0.014 0.001 HIS C 302 PHE 0.019 0.002 PHE A 968 TYR 0.025 0.002 TYR A 611 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.296 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 120 average time/residue: 1.0874 time to fit residues: 143.1104 Evaluate side-chains 96 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.3437 time to fit residues: 3.8756 ------------------------------------------------------------------------------- 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: 2.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 0.0970 chunk 127 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 94 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10790 Z= 0.162 Angle : 0.626 8.754 14649 Z= 0.322 Chirality : 0.044 0.165 1678 Planarity : 0.005 0.056 1828 Dihedral : 7.409 59.029 1566 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 3.23 % Allowed : 14.91 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -1.44 (0.23), residues: 1298 helix: 0.21 (0.22), residues: 565 sheet: -0.98 (0.38), residues: 181 loop : -2.20 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 876 HIS 0.011 0.001 HIS C 302 PHE 0.017 0.001 PHE A 968 TYR 0.025 0.001 TYR A 629 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 119 average time/residue: 1.0120 time to fit residues: 132.5621 Evaluate side-chains 103 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 6 average time/residue: 0.3162 time to fit residues: 4.0489 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 352 ASN A 810 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10790 Z= 0.373 Angle : 0.717 8.566 14649 Z= 0.366 Chirality : 0.049 0.176 1678 Planarity : 0.005 0.055 1828 Dihedral : 7.221 57.166 1566 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 3.75 % Allowed : 15.87 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1298 helix: 0.11 (0.21), residues: 577 sheet: -0.81 (0.39), residues: 174 loop : -2.11 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 876 HIS 0.006 0.001 HIS A 832 PHE 0.027 0.002 PHE A 351 TYR 0.023 0.002 TYR A 611 ARG 0.003 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 86 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 116 average time/residue: 0.9863 time to fit residues: 126.5688 Evaluate side-chains 105 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.8736 time to fit residues: 9.5497 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 580 HIS A 789 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10790 Z= 0.174 Angle : 0.623 9.097 14649 Z= 0.315 Chirality : 0.043 0.166 1678 Planarity : 0.004 0.056 1828 Dihedral : 6.546 52.971 1566 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.57 % Allowed : 16.91 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.99 (0.23), residues: 1298 helix: 0.50 (0.22), residues: 577 sheet: -0.73 (0.39), residues: 179 loop : -1.90 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 876 HIS 0.003 0.001 HIS A 798 PHE 0.017 0.001 PHE A 968 TYR 0.022 0.001 TYR A 611 ARG 0.002 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 87 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 120 average time/residue: 0.9227 time to fit residues: 123.6467 Evaluate side-chains 104 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.5062 time to fit residues: 4.7019 ------------------------------------------------------------------------------- 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: 0.3980 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10790 Z= 0.163 Angle : 0.618 12.380 14649 Z= 0.308 Chirality : 0.043 0.154 1678 Planarity : 0.004 0.056 1828 Dihedral : 6.162 52.009 1566 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.31 % Allowed : 17.61 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.72 (0.24), residues: 1298 helix: 0.71 (0.22), residues: 577 sheet: -0.51 (0.40), residues: 176 loop : -1.77 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 876 HIS 0.003 0.001 HIS A 264 PHE 0.018 0.001 PHE A 968 TYR 0.022 0.001 TYR A 611 ARG 0.003 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 89 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 115 average time/residue: 1.0694 time to fit residues: 135.4969 Evaluate side-chains 114 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.6423 time to fit residues: 7.5466 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10790 Z= 0.224 Angle : 0.650 11.067 14649 Z= 0.323 Chirality : 0.044 0.159 1678 Planarity : 0.004 0.056 1828 Dihedral : 6.138 51.842 1566 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.05 % Allowed : 18.57 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.66 (0.24), residues: 1298 helix: 0.73 (0.22), residues: 576 sheet: -0.40 (0.41), residues: 179 loop : -1.73 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 876 HIS 0.003 0.001 HIS A 832 PHE 0.019 0.001 PHE A 968 TYR 0.021 0.002 TYR A 611 ARG 0.003 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 112 average time/residue: 1.0187 time to fit residues: 126.3314 Evaluate side-chains 112 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.4785 time to fit residues: 5.8081 ------------------------------------------------------------------------------- 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: 50.0000 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 789 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10790 Z= 0.221 Angle : 0.632 11.051 14649 Z= 0.317 Chirality : 0.044 0.162 1678 Planarity : 0.004 0.053 1828 Dihedral : 6.042 51.750 1566 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.96 % Allowed : 18.40 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.66 (0.24), residues: 1298 helix: 0.75 (0.22), residues: 576 sheet: -0.41 (0.42), residues: 169 loop : -1.73 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 876 HIS 0.003 0.001 HIS A 264 PHE 0.020 0.001 PHE A 968 TYR 0.021 0.002 TYR A 611 ARG 0.003 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 86 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 109 average time/residue: 1.0081 time to fit residues: 122.2915 Evaluate side-chains 110 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.6340 time to fit residues: 7.5964 ------------------------------------------------------------------------------- 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: 0.6980 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 50 optimal weight: 50.0000 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10790 Z= 0.171 Angle : 0.613 11.076 14649 Z= 0.306 Chirality : 0.043 0.158 1678 Planarity : 0.004 0.054 1828 Dihedral : 5.771 51.903 1566 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.09 % Allowed : 19.27 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.51 (0.24), residues: 1298 helix: 0.89 (0.22), residues: 575 sheet: -0.34 (0.42), residues: 172 loop : -1.67 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 876 HIS 0.003 0.001 HIS A 264 PHE 0.018 0.001 PHE A 968 TYR 0.021 0.001 TYR A 611 ARG 0.003 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 108 average time/residue: 1.0490 time to fit residues: 125.1733 Evaluate side-chains 102 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.2194 time to fit residues: 2.2931 ------------------------------------------------------------------------------- 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: 0.5980 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 0.0370 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10790 Z= 0.179 Angle : 0.628 12.313 14649 Z= 0.310 Chirality : 0.043 0.152 1678 Planarity : 0.004 0.052 1828 Dihedral : 5.694 52.041 1566 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.18 % Allowed : 19.18 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 1298 helix: 0.96 (0.22), residues: 570 sheet: -0.29 (0.42), residues: 171 loop : -1.64 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 876 HIS 0.003 0.001 HIS A 264 PHE 0.018 0.001 PHE A 968 TYR 0.022 0.001 TYR A 611 ARG 0.005 0.000 ARG A 875 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 106 average time/residue: 1.0117 time to fit residues: 118.8167 Evaluate side-chains 105 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.6691 time to fit residues: 4.7338 ------------------------------------------------------------------------------- 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: 0.0970 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.0010 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.209555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.147426 restraints weight = 10209.496| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.46 r_work: 0.3096 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10790 Z= 0.228 Angle : 0.634 11.351 14649 Z= 0.317 Chirality : 0.044 0.160 1678 Planarity : 0.004 0.053 1828 Dihedral : 5.743 51.824 1566 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.92 % Allowed : 19.35 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.51 (0.24), residues: 1298 helix: 0.85 (0.22), residues: 576 sheet: -0.27 (0.42), residues: 172 loop : -1.67 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 876 HIS 0.003 0.001 HIS A 264 PHE 0.020 0.002 PHE A 968 TYR 0.022 0.002 TYR A 611 ARG 0.005 0.000 ARG A 875 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.17 seconds wall clock time: 62 minutes 12.22 seconds (3732.22 seconds total)