Starting phenix.real_space_refine on Tue Dec 31 21:03:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mlm_9139/12_2024/6mlm_9139.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mlm_9139/12_2024/6mlm_9139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mlm_9139/12_2024/6mlm_9139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mlm_9139/12_2024/6mlm_9139.map" model { file = "/net/cci-nas-00/data/ceres_data/6mlm_9139/12_2024/6mlm_9139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mlm_9139/12_2024/6mlm_9139.cif" } resolution = 3.5 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10416 2.51 5 N 2895 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16701 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "C" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1369 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: F, K, B, H, I, L, D, J Time building chain proxies: 8.06, per 1000 atoms: 0.48 Number of scatterers: 16701 At special positions: 0 Unit cell: (116.28, 113.22, 167.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3300 8.00 N 2895 7.00 C 10416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS C 137 " distance=2.07 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 293 " distance=2.16 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 321 " distance=2.07 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 NAG-ASN " NAG A 801 " - " ASN A 54 " " NAG A 802 " - " ASN A 256 " " NAG B 801 " - " ASN B 54 " " NAG B 802 " - " ASN B 256 " " NAG C 301 " - " ASN C 82 " " NAG D 301 " - " ASN D 82 " " NAG H 801 " - " ASN H 54 " " NAG H 802 " - " ASN H 256 " " NAG J 301 " - " ASN J 82 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.1 seconds 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3858 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 21.5% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.617A pdb=" N ASP A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 96 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'C' and resid 37 through 49 removed outlier: 4.162A pdb=" N THR C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 57 Processing helix chain 'C' and resid 74 through 127 Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.539A pdb=" N MET C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 removed outlier: 4.868A pdb=" N THR C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.616A pdb=" N ASP B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLN B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 96 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'D' and resid 37 through 49 removed outlier: 4.162A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.539A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 171 removed outlier: 4.869A pdb=" N THR D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 89 through 96 removed outlier: 3.616A pdb=" N ASP H 93 " --> pdb=" O PRO H 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN H 94 " --> pdb=" O GLN H 91 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU H 96 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 130 Processing helix chain 'H' and resid 155 through 160 Processing helix chain 'H' and resid 203 through 212 Processing helix chain 'J' and resid 37 through 49 removed outlier: 4.163A pdb=" N THR J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 57 Processing helix chain 'J' and resid 74 through 127 Processing helix chain 'J' and resid 145 through 154 removed outlier: 3.539A pdb=" N MET J 149 " --> pdb=" O ASP J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 171 removed outlier: 4.868A pdb=" N THR J 164 " --> pdb=" O THR J 160 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN J 169 " --> pdb=" O GLU J 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.104A pdb=" N ASP A 27 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 removed outlier: 3.754A pdb=" N THR A 40 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.018A pdb=" N ILE A 67 " --> pdb=" O ASP A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.414A pdb=" N THR A 75 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.553A pdb=" N ARG A 117 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N TRP A 250 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE A 195 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AB1, first strand: chain 'A' and resid 297 through 299 removed outlier: 4.081A pdb=" N CYS A 297 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.824A pdb=" N PHE E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE E 50 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'E' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.121A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.121A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.104A pdb=" N ASP B 27 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 40 through 43 removed outlier: 3.755A pdb=" N THR B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AC4, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AC5, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.017A pdb=" N ILE B 67 " --> pdb=" O ASP B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.414A pdb=" N THR B 75 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.553A pdb=" N ARG B 117 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N TRP B 250 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE B 195 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 180 through 185 Processing sheet with id=AD1, first strand: chain 'B' and resid 297 through 299 removed outlier: 4.081A pdb=" N CYS B 297 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 319 through 321 Processing sheet with id=AD3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.823A pdb=" N PHE F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'F' and resid 18 through 20 Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 24 through 27 removed outlier: 4.104A pdb=" N ASP H 27 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 40 through 43 removed outlier: 3.754A pdb=" N THR H 40 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 55 through 57 Processing sheet with id=AE4, first strand: chain 'H' and resid 59 through 60 Processing sheet with id=AE5, first strand: chain 'H' and resid 67 through 68 removed outlier: 6.018A pdb=" N ILE H 67 " --> pdb=" O ASP H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'H' and resid 75 through 76 removed outlier: 6.414A pdb=" N THR H 75 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AE8, first strand: chain 'H' and resid 116 through 118 removed outlier: 6.554A pdb=" N ARG H 117 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N TRP H 250 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE H 195 " --> pdb=" O PRO H 270 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 180 through 185 Processing sheet with id=AF1, first strand: chain 'H' and resid 297 through 299 removed outlier: 4.080A pdb=" N CYS H 297 " --> pdb=" O ILE H 304 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 319 through 321 Processing sheet with id=AF3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.824A pdb=" N PHE K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'K' and resid 18 through 20 Processing sheet with id=AF7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.120A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.120A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1737 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: 5.72 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4627 1.33 - 1.46: 4753 1.46 - 1.59: 7537 1.59 - 1.72: 0 1.72 - 1.85: 132 Bond restraints: 17049 Sorted by residual: bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" C1 NAG H 802 " pdb=" O5 NAG H 802 " ideal model delta sigma weight residual 1.406 1.550 -0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C1 NAG B 802 " pdb=" O5 NAG B 802 " ideal model delta sigma weight residual 1.406 1.550 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C1 NAG D 301 " pdb=" O5 NAG D 301 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C1 NAG C 301 " pdb=" O5 NAG C 301 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 17044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 20668 1.95 - 3.89: 1963 3.89 - 5.84: 311 5.84 - 7.78: 110 7.78 - 9.73: 9 Bond angle restraints: 23061 Sorted by residual: angle pdb=" C GLY A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta sigma weight residual 119.66 126.35 -6.69 7.30e-01 1.88e+00 8.40e+01 angle pdb=" C GLY H 88 " pdb=" N PRO H 89 " pdb=" CA PRO H 89 " ideal model delta sigma weight residual 119.66 126.33 -6.67 7.30e-01 1.88e+00 8.35e+01 angle pdb=" C GLY B 88 " pdb=" N PRO B 89 " pdb=" CA PRO B 89 " ideal model delta sigma weight residual 119.66 126.32 -6.66 7.30e-01 1.88e+00 8.32e+01 angle pdb=" C LEU H 308 " pdb=" N PRO H 309 " pdb=" CA PRO H 309 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.01e+00 9.80e-01 6.87e+01 angle pdb=" C LEU B 308 " pdb=" N PRO B 309 " pdb=" CA PRO B 309 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.01e+00 9.80e-01 6.87e+01 ... (remaining 23056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 9847 17.65 - 35.30: 306 35.30 - 52.96: 57 52.96 - 70.61: 53 70.61 - 88.26: 21 Dihedral angle restraints: 10284 sinusoidal: 4236 harmonic: 6048 Sorted by residual: dihedral pdb=" CB CYS A 297 " pdb=" SG CYS A 297 " pdb=" SG CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sinusoidal sigma weight residual -86.00 -148.65 62.65 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS A 68 " pdb=" SG CYS A 68 " pdb=" SG CYS A 293 " pdb=" CB CYS A 293 " ideal model delta sinusoidal sigma weight residual -86.00 -23.80 -62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CA GLY B 88 " pdb=" C GLY B 88 " pdb=" N PRO B 89 " pdb=" CA PRO B 89 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 10281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1778 0.055 - 0.110: 579 0.110 - 0.164: 133 0.164 - 0.219: 21 0.219 - 0.274: 6 Chirality restraints: 2517 Sorted by residual: chirality pdb=" CA CYS H 297 " pdb=" N CYS H 297 " pdb=" C CYS H 297 " pdb=" CB CYS H 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA CYS B 297 " pdb=" N CYS B 297 " pdb=" C CYS B 297 " pdb=" CB CYS B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA CYS A 297 " pdb=" N CYS A 297 " pdb=" C CYS A 297 " pdb=" CB CYS A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2514 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 54 " -0.109 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN A 54 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 54 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 54 " 0.185 2.00e-02 2.50e+03 pdb=" C1 NAG A 801 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 54 " -0.109 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN B 54 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 54 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 54 " 0.185 2.00e-02 2.50e+03 pdb=" C1 NAG B 801 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 54 " -0.108 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN H 54 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN H 54 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN H 54 " 0.185 2.00e-02 2.50e+03 pdb=" C1 NAG H 801 " -0.146 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 111 2.59 - 3.17: 14517 3.17 - 3.75: 25214 3.75 - 4.32: 36976 4.32 - 4.90: 60600 Nonbonded interactions: 137418 Sorted by model distance: nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS J 144 " pdb=" SG CYS J 148 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " model vdw 2.031 3.760 ... (remaining 137413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 36.220 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 0.145 17049 Z= 0.865 Angle : 1.310 9.731 23061 Z= 0.889 Chirality : 0.057 0.274 2517 Planarity : 0.005 0.022 3009 Dihedral : 11.419 88.259 6402 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.00 % Favored : 96.71 % Rotamer: Outliers : 0.33 % Allowed : 0.66 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2097 helix: 1.13 (0.25), residues: 336 sheet: 0.44 (0.21), residues: 537 loop : -0.01 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP I 35 HIS 0.005 0.001 HIS K 35 PHE 0.024 0.003 PHE D 24 TYR 0.029 0.004 TYR C 157 ARG 0.002 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 504 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.6336 (p) cc_final: 0.5437 (m) REVERT: C 21 TRP cc_start: 0.5789 (m-10) cc_final: 0.5275 (m-10) REVERT: C 120 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8107 (tm-30) REVERT: C 133 ASP cc_start: 0.4360 (m-30) cc_final: 0.4137 (m-30) REVERT: B 41 LYS cc_start: 0.7949 (mttt) cc_final: 0.7650 (mtmm) REVERT: B 69 THR cc_start: 0.6655 (p) cc_final: 0.6038 (m) REVERT: D 21 TRP cc_start: 0.6041 (m-10) cc_final: 0.5540 (m-10) REVERT: D 120 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8154 (tm-30) REVERT: D 132 GLU cc_start: 0.4127 (tt0) cc_final: 0.3753 (pm20) REVERT: D 133 ASP cc_start: 0.4285 (m-30) cc_final: 0.4049 (m-30) REVERT: G 104 LEU cc_start: 0.8373 (mp) cc_final: 0.8118 (mt) REVERT: H 51 GLU cc_start: 0.7793 (tt0) cc_final: 0.7581 (tp30) REVERT: H 69 THR cc_start: 0.6761 (p) cc_final: 0.5832 (m) REVERT: J 21 TRP cc_start: 0.6110 (m-10) cc_final: 0.5727 (m-10) REVERT: J 120 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8133 (tm-30) REVERT: J 132 GLU cc_start: 0.4032 (tt0) cc_final: 0.3674 (pm20) REVERT: J 152 ILE cc_start: 0.6309 (mt) cc_final: 0.6049 (mt) REVERT: L 55 GLN cc_start: 0.6402 (tp-100) cc_final: 0.6177 (tt0) REVERT: L 104 LEU cc_start: 0.8322 (mp) cc_final: 0.8118 (mt) outliers start: 6 outliers final: 1 residues processed: 509 average time/residue: 0.3691 time to fit residues: 262.7011 Evaluate side-chains 261 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN I 90 GLN B 327 GLN B 338 ASN D 12 ASN D 42 GLN D 106 HIS ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN G 90 GLN H 179 GLN H 312 ASN ** J 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17049 Z= 0.226 Angle : 0.715 11.327 23061 Z= 0.378 Chirality : 0.046 0.236 2517 Planarity : 0.005 0.045 3009 Dihedral : 6.510 69.765 2495 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.86 % Allowed : 7.74 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.08 (0.18), residues: 2097 helix: 1.18 (0.26), residues: 327 sheet: 0.63 (0.21), residues: 576 loop : -0.54 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 14 HIS 0.007 0.001 HIS D 142 PHE 0.028 0.002 PHE C 138 TYR 0.022 0.002 TYR D 119 ARG 0.007 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.6538 (p) cc_final: 0.5763 (p) REVERT: C 149 MET cc_start: 0.4340 (tpt) cc_final: 0.3468 (ppp) REVERT: B 69 THR cc_start: 0.6752 (p) cc_final: 0.5694 (p) REVERT: D 22 TYR cc_start: 0.7696 (m-80) cc_final: 0.7336 (m-80) REVERT: D 61 GLN cc_start: 0.5859 (OUTLIER) cc_final: 0.5597 (mm110) REVERT: D 149 MET cc_start: 0.4636 (tpt) cc_final: 0.4057 (ppp) REVERT: F 94 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7456 (ttm-80) REVERT: H 69 THR cc_start: 0.6634 (p) cc_final: 0.5431 (p) REVERT: J 21 TRP cc_start: 0.5404 (m-10) cc_final: 0.5196 (m-10) outliers start: 52 outliers final: 23 residues processed: 333 average time/residue: 0.3212 time to fit residues: 158.2225 Evaluate side-chains 254 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 151 optimal weight: 0.0970 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17049 Z= 0.316 Angle : 0.697 10.945 23061 Z= 0.368 Chirality : 0.045 0.292 2517 Planarity : 0.005 0.040 3009 Dihedral : 6.147 65.475 2493 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.62 % Allowed : 9.56 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2097 helix: 1.01 (0.27), residues: 321 sheet: 0.32 (0.20), residues: 549 loop : -0.90 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 21 HIS 0.005 0.001 HIS C 142 PHE 0.027 0.002 PHE L 71 TYR 0.016 0.002 TYR L 49 ARG 0.018 0.001 ARG K 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TYR cc_start: 0.7914 (m-80) cc_final: 0.7522 (m-80) REVERT: C 149 MET cc_start: 0.4544 (tpt) cc_final: 0.4263 (mmm) REVERT: B 125 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7797 (mtm-85) REVERT: D 22 TYR cc_start: 0.7491 (m-80) cc_final: 0.7237 (m-80) REVERT: F 81 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: J 115 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7515 (ttp) REVERT: K 48 MET cc_start: 0.7606 (mtm) cc_final: 0.7316 (mtm) REVERT: L 70 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.5095 (pp20) outliers start: 66 outliers final: 34 residues processed: 275 average time/residue: 0.2773 time to fit residues: 118.1333 Evaluate side-chains 252 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 115 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain L residue 70 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.0060 chunk 141 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17049 Z= 0.209 Angle : 0.637 10.512 23061 Z= 0.333 Chirality : 0.043 0.190 2517 Planarity : 0.004 0.035 3009 Dihedral : 5.795 58.372 2493 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.24 % Allowed : 11.53 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2097 helix: 0.86 (0.27), residues: 321 sheet: 0.36 (0.21), residues: 528 loop : -0.94 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 21 HIS 0.006 0.001 HIS J 142 PHE 0.014 0.002 PHE F 63 TYR 0.017 0.001 TYR C 157 ARG 0.015 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 TRP cc_start: 0.5571 (m-10) cc_final: 0.5058 (m-10) REVERT: C 149 MET cc_start: 0.4530 (tpt) cc_final: 0.4237 (mmm) REVERT: D 22 TYR cc_start: 0.7520 (m-80) cc_final: 0.7237 (m-80) REVERT: D 103 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8496 (mp0) REVERT: G 11 LEU cc_start: 0.6794 (mp) cc_final: 0.6270 (tt) REVERT: G 70 GLU cc_start: 0.5375 (tm-30) cc_final: 0.5104 (pp20) REVERT: J 102 MET cc_start: 0.8406 (mtp) cc_final: 0.8179 (mtp) REVERT: J 115 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7421 (ttp) REVERT: L 70 GLU cc_start: 0.5393 (tm-30) cc_final: 0.5122 (pp20) outliers start: 59 outliers final: 37 residues processed: 267 average time/residue: 0.2891 time to fit residues: 117.6376 Evaluate side-chains 239 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 115 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 138 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 102 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN K 3 GLN K 6 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17049 Z= 0.459 Angle : 0.772 9.297 23061 Z= 0.407 Chirality : 0.046 0.195 2517 Planarity : 0.006 0.043 3009 Dihedral : 6.347 36.997 2493 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.79 % Allowed : 13.29 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.12 (0.17), residues: 2097 helix: 0.39 (0.27), residues: 318 sheet: -0.20 (0.21), residues: 480 loop : -1.29 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP J 21 HIS 0.007 0.002 HIS H 199 PHE 0.022 0.003 PHE B 263 TYR 0.024 0.003 TYR I 49 ARG 0.017 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7240 (ttp-110) cc_final: 0.6838 (ttm110) REVERT: C 21 TRP cc_start: 0.5811 (m-10) cc_final: 0.5428 (m-10) REVERT: C 106 HIS cc_start: 0.8245 (m-70) cc_final: 0.8027 (m90) REVERT: D 103 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8499 (mp0) REVERT: D 120 GLU cc_start: 0.8013 (pt0) cc_final: 0.7714 (pp20) REVERT: F 81 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: G 100 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6804 (pt0) REVERT: J 22 TYR cc_start: 0.7699 (m-80) cc_final: 0.7212 (m-80) REVERT: K 48 MET cc_start: 0.7481 (mtm) cc_final: 0.7154 (mtm) REVERT: L 70 GLU cc_start: 0.5555 (tm-30) cc_final: 0.5276 (pp20) outliers start: 69 outliers final: 41 residues processed: 254 average time/residue: 0.3081 time to fit residues: 121.0392 Evaluate side-chains 241 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17049 Z= 0.224 Angle : 0.635 8.995 23061 Z= 0.333 Chirality : 0.043 0.201 2517 Planarity : 0.004 0.044 3009 Dihedral : 5.775 33.173 2493 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.51 % Allowed : 13.45 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.06 (0.17), residues: 2097 helix: 0.56 (0.27), residues: 318 sheet: -0.32 (0.21), residues: 504 loop : -1.22 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 47 HIS 0.006 0.001 HIS D 142 PHE 0.025 0.002 PHE B 263 TYR 0.018 0.001 TYR C 157 ARG 0.014 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6690 (ttp-110) REVERT: C 21 TRP cc_start: 0.5879 (m-10) cc_final: 0.5520 (m-10) REVERT: C 106 HIS cc_start: 0.8207 (m-70) cc_final: 0.7978 (m90) REVERT: I 11 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6225 (pp) REVERT: B 130 ARG cc_start: 0.6799 (ttp-110) cc_final: 0.6392 (ttm110) REVERT: D 102 MET cc_start: 0.8485 (mtp) cc_final: 0.8277 (mtp) REVERT: D 103 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8537 (mp0) REVERT: D 120 GLU cc_start: 0.8012 (pt0) cc_final: 0.7765 (pp20) REVERT: J 21 TRP cc_start: 0.4948 (m-10) cc_final: 0.4281 (m-10) REVERT: J 22 TYR cc_start: 0.7492 (m-80) cc_final: 0.7272 (m-80) REVERT: K 48 MET cc_start: 0.7385 (mtm) cc_final: 0.7116 (mtm) REVERT: L 70 GLU cc_start: 0.5620 (tm-30) cc_final: 0.5300 (pp20) outliers start: 64 outliers final: 44 residues processed: 259 average time/residue: 0.2899 time to fit residues: 116.0429 Evaluate side-chains 241 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 263 PHE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 119 TYR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17049 Z= 0.183 Angle : 0.606 8.295 23061 Z= 0.317 Chirality : 0.043 0.213 2517 Planarity : 0.004 0.041 3009 Dihedral : 5.399 29.007 2493 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.73 % Allowed : 14.00 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2097 helix: 0.81 (0.28), residues: 318 sheet: -0.22 (0.22), residues: 483 loop : -1.13 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 21 HIS 0.006 0.001 HIS D 142 PHE 0.019 0.002 PHE A 298 TYR 0.016 0.001 TYR C 157 ARG 0.011 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.6826 (ttp-110) cc_final: 0.6552 (ttp-110) REVERT: C 21 TRP cc_start: 0.5801 (m-10) cc_final: 0.5476 (m-10) REVERT: C 106 HIS cc_start: 0.8169 (m-70) cc_final: 0.7941 (m90) REVERT: I 105 GLU cc_start: 0.7268 (mp0) cc_final: 0.7019 (mp0) REVERT: B 130 ARG cc_start: 0.6750 (ttp-110) cc_final: 0.6375 (ttm110) REVERT: B 139 MET cc_start: 0.7258 (ttm) cc_final: 0.6984 (ttm) REVERT: G 105 GLU cc_start: 0.7074 (mp0) cc_final: 0.6595 (mp0) REVERT: H 139 MET cc_start: 0.7259 (ttm) cc_final: 0.7032 (ttm) REVERT: H 217 LEU cc_start: 0.8512 (tt) cc_final: 0.8288 (tp) REVERT: J 21 TRP cc_start: 0.4888 (m-10) cc_final: 0.4531 (m-10) REVERT: K 39 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: K 48 MET cc_start: 0.7490 (mtm) cc_final: 0.7269 (mtm) REVERT: L 70 GLU cc_start: 0.5624 (tm-30) cc_final: 0.5283 (pp20) outliers start: 68 outliers final: 43 residues processed: 257 average time/residue: 0.2881 time to fit residues: 112.4670 Evaluate side-chains 243 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 263 PHE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 119 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17049 Z= 0.242 Angle : 0.639 8.628 23061 Z= 0.334 Chirality : 0.043 0.269 2517 Planarity : 0.004 0.059 3009 Dihedral : 5.459 27.135 2493 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.40 % Allowed : 14.99 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2097 helix: 0.97 (0.28), residues: 315 sheet: -0.03 (0.23), residues: 459 loop : -1.17 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 21 HIS 0.007 0.001 HIS D 142 PHE 0.020 0.002 PHE B 263 TYR 0.020 0.001 TYR C 157 ARG 0.009 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6751 (ttp-110) REVERT: C 21 TRP cc_start: 0.6110 (m-10) cc_final: 0.5682 (m-10) REVERT: C 88 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8219 (mtm) REVERT: C 106 HIS cc_start: 0.8173 (m-70) cc_final: 0.7913 (m90) REVERT: I 105 GLU cc_start: 0.7250 (mp0) cc_final: 0.6908 (mp0) REVERT: B 130 ARG cc_start: 0.6843 (ttp-110) cc_final: 0.6463 (ttm110) REVERT: G 70 GLU cc_start: 0.6125 (tm-30) cc_final: 0.5881 (tm-30) REVERT: G 100 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6789 (pt0) REVERT: G 105 GLU cc_start: 0.7149 (mp0) cc_final: 0.6332 (mp0) REVERT: H 41 LYS cc_start: 0.7530 (tmmt) cc_final: 0.7327 (tmmt) REVERT: H 217 LEU cc_start: 0.8576 (tt) cc_final: 0.8357 (tp) REVERT: K 39 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.6936 (tt0) REVERT: K 48 MET cc_start: 0.7518 (mtm) cc_final: 0.7238 (mtm) REVERT: L 70 GLU cc_start: 0.5804 (tm-30) cc_final: 0.5492 (pp20) outliers start: 62 outliers final: 49 residues processed: 246 average time/residue: 0.2921 time to fit residues: 109.5048 Evaluate side-chains 252 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 263 PHE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 119 TYR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN A 312 ASN E 6 GLN D 12 ASN D 28 ASN D 79 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN J 28 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 17049 Z= 0.482 Angle : 0.794 9.151 23061 Z= 0.420 Chirality : 0.048 0.239 2517 Planarity : 0.006 0.090 3009 Dihedral : 6.284 36.518 2493 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.90 % Allowed : 14.66 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.49 (0.17), residues: 2097 helix: 0.39 (0.28), residues: 318 sheet: -0.69 (0.22), residues: 480 loop : -1.51 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP J 21 HIS 0.007 0.002 HIS D 142 PHE 0.029 0.003 PHE B 263 TYR 0.023 0.003 TYR I 49 ARG 0.013 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7104 (ttp-110) cc_final: 0.6831 (ttm110) REVERT: A 336 MET cc_start: 0.6203 (ptp) cc_final: 0.5177 (ppp) REVERT: C 88 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8212 (mtm) REVERT: C 128 GLU cc_start: 0.5150 (mp0) cc_final: 0.4640 (tt0) REVERT: C 149 MET cc_start: 0.4269 (tpt) cc_final: 0.3979 (tpt) REVERT: E 39 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7237 (tp40) REVERT: D 28 ASN cc_start: 0.5449 (OUTLIER) cc_final: 0.5165 (m-40) REVERT: G 100 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6796 (pt0) REVERT: G 105 GLU cc_start: 0.7455 (mp0) cc_final: 0.7086 (mp0) REVERT: J 28 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5695 (m-40) REVERT: K 23 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (ptpt) REVERT: K 39 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: K 48 MET cc_start: 0.7586 (mtm) cc_final: 0.7292 (mtm) outliers start: 71 outliers final: 49 residues processed: 245 average time/residue: 0.2825 time to fit residues: 105.9446 Evaluate side-chains 247 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 263 PHE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17049 Z= 0.202 Angle : 0.677 9.990 23061 Z= 0.355 Chirality : 0.044 0.216 2517 Planarity : 0.005 0.068 3009 Dihedral : 5.663 30.490 2493 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.42 % Allowed : 16.53 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.21 (0.18), residues: 2097 helix: 0.78 (0.28), residues: 318 sheet: -0.59 (0.22), residues: 504 loop : -1.35 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 21 HIS 0.007 0.001 HIS D 142 PHE 0.021 0.002 PHE B 263 TYR 0.025 0.001 TYR C 157 ARG 0.010 0.001 ARG J 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.6956 (ttp-110) cc_final: 0.6711 (ttp-110) REVERT: C 21 TRP cc_start: 0.6320 (m-10) cc_final: 0.6021 (m-10) REVERT: C 88 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8254 (mtm) REVERT: C 128 GLU cc_start: 0.5151 (mp0) cc_final: 0.4613 (tt0) REVERT: C 149 MET cc_start: 0.4317 (tpt) cc_final: 0.4083 (mmm) REVERT: D 103 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8538 (mp0) REVERT: G 11 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5924 (pp) REVERT: G 70 GLU cc_start: 0.6089 (tm-30) cc_final: 0.5889 (tm-30) REVERT: G 100 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6854 (pt0) REVERT: G 105 GLU cc_start: 0.7268 (mp0) cc_final: 0.6896 (mp0) REVERT: H 217 LEU cc_start: 0.8568 (tt) cc_final: 0.8353 (tp) REVERT: K 39 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7000 (tt0) outliers start: 44 outliers final: 31 residues processed: 245 average time/residue: 0.2970 time to fit residues: 109.1136 Evaluate side-chains 236 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 PHE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 119 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.0000 chunk 50 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 144 optimal weight: 0.0470 overall best weight: 2.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.147467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121735 restraints weight = 37298.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.122724 restraints weight = 26727.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123911 restraints weight = 21193.346| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17049 Z= 0.287 Angle : 0.695 9.382 23061 Z= 0.365 Chirality : 0.045 0.367 2517 Planarity : 0.005 0.083 3009 Dihedral : 5.794 31.450 2493 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.80 % Allowed : 16.20 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.28 (0.17), residues: 2097 helix: 0.75 (0.28), residues: 318 sheet: -0.65 (0.22), residues: 504 loop : -1.39 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 21 HIS 0.007 0.001 HIS D 142 PHE 0.022 0.002 PHE E 63 TYR 0.021 0.002 TYR C 157 ARG 0.013 0.001 ARG J 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.59 seconds wall clock time: 62 minutes 31.72 seconds (3751.72 seconds total)