Starting phenix.real_space_refine on Sat Dec 9 09:21:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2023/6k7l_9939.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2023/6k7l_9939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2023/6k7l_9939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2023/6k7l_9939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2023/6k7l_9939.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7l_9939/12_2023/6k7l_9939.pdb" } resolution = 2.83 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 Mg 1 5.21 5 S 54 5.16 5 Be 1 3.05 5 C 6881 2.51 5 N 1756 2.21 5 O 1919 1.98 5 F 3 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 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 327": "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 GLU 364": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "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 TYR 908": "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 PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ASP 281": "OD1" <-> "OD2" 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 ASP 305": "OD1" <-> "OD2" 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: 10615 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7893 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 961} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, '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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'BEF': 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: 6.05, per 1000 atoms: 0.57 Number of scatterers: 10615 At special positions: 0 Unit cell: (73.04, 107.07, 166.83, 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 54 16.00 Mg 1 11.99 F 3 9.00 O 1919 8.00 N 1756 7.00 C 6881 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.04 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=1, 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 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 1.9 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 49.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 4.137A pdb=" N LEU A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 101 through 132 removed outlier: 4.932A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) 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 185 through 190 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.437A pdb=" N ILE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.568A pdb=" N ILE A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.996A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.571A 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 448 through 455 Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.925A pdb=" N ILE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 564 removed outlier: 3.722A pdb=" N TYR A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 600 through 617 removed outlier: 3.892A pdb=" N THR A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 632 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 739 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 762 through 775 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.320A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 856 removed outlier: 3.730A pdb=" N LEU A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.897A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 Processing helix chain 'A' and resid 887 through 896 removed outlier: 3.914A 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: 3.574A pdb=" N THR A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 918 " --> pdb=" O THR A 914 " (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: 3.835A 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: 3.547A pdb=" N MET A1023 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1024 " --> pdb=" O PRO A1021 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1020 through 1024' Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'A' and resid 1033 through 1062 removed outlier: 4.055A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.102A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.562A pdb=" N CYS C 94 " --> pdb=" O CYS C 91 " (cutoff:3.500A) 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: 3.515A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.865A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 252 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) 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 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.556A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.645A pdb=" N TYR A 182 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.697A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS A 759 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 729 " --> pdb=" O CYS A 759 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASP A 730 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 696 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.638A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS A 424 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA8, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.970A pdb=" N THR A 547 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 79 removed outlier: 7.056A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 110 removed outlier: 4.749A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 497 hydrogen bonds defined for protein. 1437 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: 3.78 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1815 1.32 - 1.44: 2878 1.44 - 1.57: 6083 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10861 Sorted by residual: bond pdb=" F2 BEF A1801 " pdb="BE BEF A1801 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" F1 BEF A1801 " pdb="BE BEF A1801 " ideal model delta sigma weight residual 1.476 1.758 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" F3 BEF A1801 " pdb="BE BEF A1801 " ideal model delta sigma weight residual 1.476 1.756 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C ARG C 215 " pdb=" N ASN C 216 " ideal model delta sigma weight residual 1.329 1.218 0.111 1.86e-02 2.89e+03 3.53e+01 bond pdb=" CB VAL A 853 " pdb=" CG1 VAL A 853 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.79e+00 ... (remaining 10856 not shown) Histogram of bond angle deviations from ideal: 96.33 - 103.98: 160 103.98 - 111.64: 4521 111.64 - 119.29: 4442 119.29 - 126.94: 5468 126.94 - 134.59: 148 Bond angle restraints: 14739 Sorted by residual: angle pdb=" C LEU A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 121.54 133.10 -11.56 1.91e+00 2.74e-01 3.66e+01 angle pdb=" N SER A 223 " pdb=" CA SER A 223 " pdb=" C SER A 223 " ideal model delta sigma weight residual 109.81 120.43 -10.62 2.21e+00 2.05e-01 2.31e+01 angle pdb=" N SER A1024 " pdb=" CA SER A1024 " pdb=" C SER A1024 " ideal model delta sigma weight residual 112.38 117.89 -5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" C ILE A 235 " pdb=" N ARG A 236 " pdb=" CA ARG A 236 " ideal model delta sigma weight residual 121.70 129.52 -7.82 1.80e+00 3.09e-01 1.89e+01 angle pdb=" N THR A 135 " pdb=" CA THR A 135 " pdb=" C THR A 135 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.70e+01 ... (remaining 14734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 6036 22.07 - 44.13: 436 44.13 - 66.20: 58 66.20 - 88.26: 18 88.26 - 110.33: 1 Dihedral angle restraints: 6549 sinusoidal: 2710 harmonic: 3839 Sorted by residual: dihedral pdb=" CA ILE A 485 " pdb=" C ILE A 485 " pdb=" N TYR A 486 " pdb=" CA TYR A 486 " ideal model delta harmonic sigma weight residual -180.00 -130.47 -49.53 0 5.00e+00 4.00e-02 9.81e+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 -134.93 -45.07 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA GLY A 336 " pdb=" C GLY A 336 " pdb=" N ALA A 337 " pdb=" CA ALA A 337 " ideal model delta harmonic sigma weight residual -180.00 -147.63 -32.37 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 6546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1259 0.071 - 0.142: 379 0.142 - 0.213: 38 0.213 - 0.284: 5 0.284 - 0.355: 3 Chirality restraints: 1684 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB ILE A 485 " pdb=" CA ILE A 485 " pdb=" CG1 ILE A 485 " pdb=" CG2 ILE A 485 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CG LEU A 529 " pdb=" CB LEU A 529 " pdb=" CD1 LEU A 529 " pdb=" CD2 LEU A 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1681 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " -0.262 2.00e-02 2.50e+03 2.20e-01 6.06e+02 pdb=" C7 NAG C 405 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.132 2.00e-02 2.50e+03 1.14e-01 1.64e+02 pdb=" C7 NAG B 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.067 2.00e-02 2.50e+03 5.53e-02 3.82e+01 pdb=" C7 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.088 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.011 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 70 2.56 - 3.15: 7857 3.15 - 3.73: 16812 3.73 - 4.32: 24631 4.32 - 4.90: 40210 Nonbonded interactions: 89580 Sorted by model distance: nonbonded pdb=" F3 BEF A1801 " pdb="MG MG A1802 " model vdw 1.976 2.120 nonbonded pdb=" OD1 ASP A 786 " pdb="MG MG A1802 " model vdw 2.077 2.170 nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1802 " model vdw 2.096 2.170 nonbonded pdb=" O THR A 411 " pdb="MG MG A1802 " model vdw 2.132 2.170 nonbonded pdb=" OD2 ASP A 409 " pdb=" F3 BEF A1801 " model vdw 2.187 2.390 ... (remaining 89575 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.250 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.750 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: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.284 10861 Z= 0.740 Angle : 1.151 11.558 14739 Z= 0.612 Chirality : 0.065 0.355 1684 Planarity : 0.011 0.220 1841 Dihedral : 15.492 110.326 4064 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.46 % Favored : 92.31 % Rotamer: Outliers : 0.17 % Allowed : 7.21 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.27 (0.19), residues: 1301 helix: -2.16 (0.16), residues: 612 sheet: -0.76 (0.39), residues: 181 loop : -2.54 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 607 HIS 0.012 0.002 HIS A 147 PHE 0.027 0.004 PHE C 179 TYR 0.030 0.004 TYR C 297 ARG 0.014 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.280 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 1.3339 time to fit residues: 193.3828 Evaluate side-chains 96 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 147 HIS ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN A 323 HIS A 352 ASN A 433 GLN A 765 GLN A 776 GLN A 838 ASN A1127 ASN C 36 GLN C 176 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10861 Z= 0.199 Angle : 0.660 9.286 14739 Z= 0.339 Chirality : 0.045 0.397 1684 Planarity : 0.005 0.079 1841 Dihedral : 8.344 105.145 1576 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 1.91 % Allowed : 11.38 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.72 (0.22), residues: 1301 helix: -0.52 (0.20), residues: 612 sheet: -0.32 (0.40), residues: 180 loop : -2.16 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.004 0.001 HIS A 147 PHE 0.020 0.002 PHE A 968 TYR 0.014 0.001 TYR C 122 ARG 0.002 0.000 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.267 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 123 average time/residue: 1.1984 time to fit residues: 160.3964 Evaluate side-chains 114 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.8647 time to fit residues: 5.4726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 95 optimal weight: 0.5980 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 134 GLN A 187 ASN A 679 ASN A 765 GLN A 776 GLN A1118 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10861 Z= 0.172 Angle : 0.611 8.853 14739 Z= 0.312 Chirality : 0.044 0.402 1684 Planarity : 0.005 0.075 1841 Dihedral : 7.703 98.324 1576 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 2.26 % Allowed : 13.47 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.92 (0.23), residues: 1301 helix: 0.26 (0.21), residues: 619 sheet: -0.12 (0.40), residues: 187 loop : -1.88 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 456 PHE 0.019 0.001 PHE A 968 TYR 0.014 0.001 TYR C 122 ARG 0.010 0.000 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.203 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 128 average time/residue: 1.2387 time to fit residues: 172.0582 Evaluate side-chains 117 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1639 time to fit residues: 2.7911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 113 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 456 HIS A 765 GLN A 776 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10861 Z= 0.142 Angle : 0.575 9.929 14739 Z= 0.295 Chirality : 0.043 0.373 1684 Planarity : 0.004 0.073 1841 Dihedral : 7.060 84.797 1576 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 2.00 % Allowed : 15.55 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.49 (0.24), residues: 1301 helix: 0.70 (0.22), residues: 615 sheet: 0.04 (0.40), residues: 187 loop : -1.76 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 456 PHE 0.017 0.001 PHE A 968 TYR 0.011 0.001 TYR C 122 ARG 0.016 0.000 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.187 Fit side-chains outliers start: 23 outliers final: 7 residues processed: 132 average time/residue: 1.2255 time to fit residues: 175.6449 Evaluate side-chains 120 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1617 time to fit residues: 2.4506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10861 Z= 0.233 Angle : 0.619 10.060 14739 Z= 0.317 Chirality : 0.045 0.348 1684 Planarity : 0.005 0.071 1841 Dihedral : 7.055 75.045 1576 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 2.43 % Allowed : 16.07 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.41 (0.24), residues: 1301 helix: 0.70 (0.21), residues: 620 sheet: 0.14 (0.40), residues: 184 loop : -1.68 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 927 HIS 0.005 0.001 HIS A 456 PHE 0.020 0.002 PHE A 968 TYR 0.017 0.001 TYR C 297 ARG 0.009 0.000 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.203 Fit side-chains outliers start: 28 outliers final: 8 residues processed: 131 average time/residue: 1.1138 time to fit residues: 159.2741 Evaluate side-chains 118 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.1527 time to fit residues: 2.5013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10861 Z= 0.175 Angle : 0.586 9.230 14739 Z= 0.302 Chirality : 0.043 0.231 1684 Planarity : 0.004 0.071 1841 Dihedral : 6.444 51.531 1576 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 1.74 % Allowed : 17.72 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.20 (0.24), residues: 1301 helix: 0.91 (0.22), residues: 614 sheet: 0.32 (0.40), residues: 191 loop : -1.65 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 456 PHE 0.019 0.001 PHE A 968 TYR 0.013 0.001 TYR C 122 ARG 0.015 0.000 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 125 average time/residue: 1.1547 time to fit residues: 157.5909 Evaluate side-chains 118 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1602 time to fit residues: 2.5048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10861 Z= 0.159 Angle : 0.578 8.528 14739 Z= 0.296 Chirality : 0.042 0.145 1684 Planarity : 0.004 0.070 1841 Dihedral : 5.909 39.487 1576 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 1.56 % Allowed : 18.59 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.10 (0.24), residues: 1301 helix: 0.96 (0.22), residues: 620 sheet: 0.40 (0.40), residues: 190 loop : -1.60 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 456 PHE 0.018 0.001 PHE A 968 TYR 0.012 0.001 TYR C 122 ARG 0.016 0.000 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 1.2010 time to fit residues: 166.3846 Evaluate side-chains 117 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1101 time to fit residues: 2.0068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10861 Z= 0.274 Angle : 0.636 8.265 14739 Z= 0.327 Chirality : 0.045 0.147 1684 Planarity : 0.005 0.070 1841 Dihedral : 6.171 42.296 1576 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 1.74 % Allowed : 18.85 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.25 (0.24), residues: 1301 helix: 0.80 (0.21), residues: 619 sheet: 0.39 (0.40), residues: 190 loop : -1.64 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 260 HIS 0.004 0.001 HIS A 456 PHE 0.022 0.002 PHE A 968 TYR 0.017 0.002 TYR C 297 ARG 0.017 0.001 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 1.3399 time to fit residues: 185.5641 Evaluate side-chains 118 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.4920 time to fit residues: 4.3496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 0.0570 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10861 Z= 0.160 Angle : 0.577 7.424 14739 Z= 0.298 Chirality : 0.042 0.148 1684 Planarity : 0.004 0.075 1841 Dihedral : 5.648 39.253 1576 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.22 % Allowed : 19.98 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.03 (0.24), residues: 1301 helix: 1.00 (0.22), residues: 620 sheet: 0.52 (0.40), residues: 193 loop : -1.60 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 456 PHE 0.018 0.001 PHE A 968 TYR 0.012 0.001 TYR C 122 ARG 0.018 0.000 ARG A1059 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 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: 14 poor density : 116 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 128 average time/residue: 1.2338 time to fit residues: 171.8577 Evaluate side-chains 122 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1033 time to fit residues: 1.8506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.0470 chunk 63 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10861 Z= 0.171 Angle : 0.593 10.094 14739 Z= 0.303 Chirality : 0.043 0.177 1684 Planarity : 0.004 0.076 1841 Dihedral : 5.562 39.367 1576 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.96 % Allowed : 20.33 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.05 (0.24), residues: 1301 helix: 1.06 (0.22), residues: 619 sheet: 0.62 (0.40), residues: 190 loop : -1.55 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 456 PHE 0.018 0.001 PHE A 968 TYR 0.012 0.001 TYR C 122 ARG 0.018 0.000 ARG A1059 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 1.2345 time to fit residues: 161.2405 Evaluate side-chains 115 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.6823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.190809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149645 restraints weight = 10028.321| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.31 r_work: 0.3177 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10861 Z= 0.242 Angle : 0.627 12.498 14739 Z= 0.320 Chirality : 0.044 0.145 1684 Planarity : 0.005 0.073 1841 Dihedral : 5.795 40.486 1576 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 1.22 % Allowed : 19.90 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.05 (0.24), residues: 1301 helix: 0.94 (0.21), residues: 618 sheet: 0.62 (0.40), residues: 190 loop : -1.57 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 927 HIS 0.005 0.001 HIS A 456 PHE 0.020 0.002 PHE A 968 TYR 0.016 0.001 TYR C 122 ARG 0.018 0.000 ARG A1059 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3466.99 seconds wall clock time: 62 minutes 54.40 seconds (3774.40 seconds total)