Starting phenix.real_space_refine on Sat Sep 12 15:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_9139.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_9139.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_9139.cif" model { file = "/net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_9139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_9139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_9139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mlm_9139/09_2026/6mlm_9139.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: "I" 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 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 chiralities: 1 Restraints were copied for chains: B, H, D, J, F, K, G, L Time building chain proxies: 3.38, per 1000 atoms: 0.20 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=24, 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 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS D 137 " distance=2.07 Simple disulfide: pdb=" SG CYS H 30 " - pdb=" SG CYS J 137 " distance=2.07 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 293 " distance=2.16 Simple disulfide: pdb=" SG CYS H 68 " - pdb=" SG CYS H 293 " distance=2.16 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 321 " distance=2.07 Simple disulfide: pdb=" SG CYS H 297 " - pdb=" SG CYS H 321 " distance=2.07 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.02 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 148 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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: 1.26 Conformation dependent library (CDL) restraints added in 704.3 milliseconds 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: 0.43 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: 2.52 Time building geometry restraints manager: 1.71 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: 9689 17.65 - 35.30: 307 35.30 - 52.96: 69 52.96 - 70.61: 57 70.61 - 88.26: 21 Dihedral angle restraints: 10143 sinusoidal: 4095 harmonic: 6048 Sorted by residual: dihedral pdb=" CB CYS H 297 " pdb=" SG CYS H 297 " pdb=" SG CYS H 321 " pdb=" CB CYS H 321 " ideal model delta sinusoidal sigma weight residual -86.00 -148.66 62.66 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS B 297 " pdb=" SG CYS B 297 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual -86.00 -148.66 62.66 1 1.00e+01 1.00e-02 5.19e+01 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 ... (remaining 10140 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: 2.28 - 2.80: 4528 2.80 - 3.33: 15042 3.33 - 3.85: 28138 3.85 - 4.38: 33103 4.38 - 4.90: 56559 Nonbonded interactions: 137370 Sorted by model distance: nonbonded pdb=" O ASP J 174 " pdb=" OD1 ASP J 174 " model vdw 2.276 3.040 nonbonded pdb=" O ASP C 174 " pdb=" OD1 ASP C 174 " model vdw 2.277 3.040 nonbonded pdb=" O ASP D 174 " pdb=" OD1 ASP D 174 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR K 99 " pdb=" OD1 ASN L 34 " model vdw 2.372 3.040 nonbonded pdb=" OH TYR F 99 " pdb=" OD1 ASN G 34 " model vdw 2.372 3.040 ... (remaining 137365 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: 0.03 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 'I' selection = chain 'G' 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 17082 Z= 0.709 Angle : 1.362 16.115 23136 Z= 0.905 Chirality : 0.057 0.274 2517 Planarity : 0.005 0.022 3009 Dihedral : 11.523 88.259 6213 Min Nonbonded Distance : 2.276 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG G 61 TYR 0.029 0.004 TYR C 157 PHE 0.024 0.003 PHE D 24 TRP 0.033 0.004 TRP I 35 HIS 0.005 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01321 / 0.70 (17049) covalent geometry : angle 1.31031 / 0.89 (23061) SS BOND : bond 0.04934 / 2.38 ( 24) SS BOND : angle 7.86537 / 5.11 ( 48) hydrogen bonds : bond 0.17918 / 11.62 ( 663) hydrogen bonds : angle 7.95945 / 5.56 ( 1737) link_NAG-ASN : bond 0.06533 / 4.04 ( 9) link_NAG-ASN : angle 3.75946 / 2.58 ( 27) *********************** 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 : 0.656 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: 0.6335 (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: 0.1471 time to fit residues: 106.4457 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 : 0.714 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN I 90 GLN B 327 GLN B 338 ASN D 42 GLN D 106 HIS F 3 GLN G 90 GLN H 179 GLN H 312 ASN L 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.153628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.127580 restraints weight = 36427.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130291 restraints weight = 23567.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130903 restraints weight = 16076.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131506 restraints weight = 12691.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131710 restraints weight = 11371.603| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17082 Z= 0.173 Angle : 0.744 10.117 23136 Z= 0.389 Chirality : 0.046 0.221 2517 Planarity : 0.005 0.045 3009 Dihedral : 5.853 58.215 2306 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.80 % Allowed : 7.41 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2097 helix: 1.20 (0.26), residues: 327 sheet: 0.62 (0.21), residues: 576 loop : -0.50 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 54 TYR 0.020 0.002 TYR C 157 PHE 0.027 0.002 PHE D 138 TRP 0.012 0.001 TRP D 14 HIS 0.006 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (17049) covalent geometry : angle 0.72359 / 0.38 (23061) SS BOND : bond 0.00419 / 0.27 ( 24) SS BOND : angle 2.90088 / 1.82 ( 48) hydrogen bonds : bond 0.06084 / 3.96 ( 663) hydrogen bonds : angle 6.54661 / 4.61 ( 1737) link_NAG-ASN : bond 0.00215 / 0.12 ( 9) link_NAG-ASN : angle 3.41665 / 2.34 ( 27) *********************** 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 360 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 309 time to evaluate : 0.597 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 69 THR cc_start: 0.6635 (p) cc_final: 0.5499 (p) REVERT: C 149 MET cc_start: 0.4262 (tpt) cc_final: 0.3482 (ptt) REVERT: B 69 THR cc_start: 0.6761 (p) cc_final: 0.6384 (p) REVERT: D 61 GLN cc_start: 0.5781 (OUTLIER) cc_final: 0.5490 (mm110) REVERT: D 115 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.7041 (ttp) REVERT: D 149 MET cc_start: 0.4167 (tpt) cc_final: 0.3671 (ptt) REVERT: F 23 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8496 (mtpp) REVERT: H 69 THR cc_start: 0.6731 (p) cc_final: 0.5211 (p) REVERT: J 149 MET cc_start: 0.4491 (tpt) cc_final: 0.4011 (ptt) REVERT: K 48 MET cc_start: 0.7477 (mtm) cc_final: 0.7250 (mtm) outliers start: 51 outliers final: 23 residues processed: 332 average time/residue: 0.1262 time to fit residues: 63.3897 Evaluate side-chains 254 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 271 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 115 MET 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 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 137 optimal weight: 7.9990 chunk 172 optimal weight: 0.0770 chunk 2 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 GLN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.143711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119218 restraints weight = 37575.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.119139 restraints weight = 23607.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120150 restraints weight = 21485.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.120644 restraints weight = 15926.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120735 restraints weight = 14879.425| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17082 Z= 0.267 Angle : 0.768 9.492 23136 Z= 0.404 Chirality : 0.046 0.215 2517 Planarity : 0.005 0.043 3009 Dihedral : 5.821 30.417 2304 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.95 % Allowed : 9.61 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2097 helix: 0.87 (0.27), residues: 321 sheet: 0.10 (0.21), residues: 534 loop : -1.02 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 54 TYR 0.020 0.002 TYR H 143 PHE 0.028 0.003 PHE L 71 TRP 0.029 0.003 TRP C 21 HIS 0.006 0.002 HIS H 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 (17049) covalent geometry : angle 0.75436 / 0.40 (23061) SS BOND : bond 0.00809 / 0.61 ( 24) SS BOND : angle 2.50000 / 1.54 ( 48) hydrogen bonds : bond 0.05863 / 3.83 ( 663) hydrogen bonds : angle 6.31474 / 4.46 ( 1737) link_NAG-ASN : bond 0.00471 / 0.31 ( 9) link_NAG-ASN : angle 2.90223 / 1.72 ( 27) *********************** 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 320 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 248 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 GLU cc_start: 0.2175 (mt-10) cc_final: 0.1644 (mt-10) REVERT: C 22 TYR cc_start: 0.8178 (m-80) cc_final: 0.7864 (m-80) REVERT: E 96 MET cc_start: 0.6779 (tpt) cc_final: 0.6540 (tpt) REVERT: D 115 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6803 (ttp) REVERT: F 68 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8387 (mm) REVERT: J 115 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7119 (ttp) REVERT: L 70 GLU cc_start: 0.5226 (OUTLIER) cc_final: 0.4981 (pp20) REVERT: L 104 LEU cc_start: 0.8096 (mp) cc_final: 0.7773 (mt) outliers start: 72 outliers final: 37 residues processed: 283 average time/residue: 0.1123 time to fit residues: 50.0649 Evaluate side-chains 258 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 258 THR 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 127 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 115 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 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 327 GLN Chi-restraints excluded: chain H residue 329 SER 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 195 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.0060 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.146138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.121199 restraints weight = 37127.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.122195 restraints weight = 25062.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122960 restraints weight = 19712.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.123473 restraints weight = 14854.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.124209 restraints weight = 13591.049| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17082 Z= 0.157 Angle : 0.665 9.060 23136 Z= 0.344 Chirality : 0.043 0.208 2517 Planarity : 0.004 0.056 3009 Dihedral : 5.467 31.871 2304 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.91 % Allowed : 12.25 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2097 helix: 0.92 (0.27), residues: 318 sheet: 0.20 (0.21), residues: 528 loop : -0.98 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 54 TYR 0.021 0.001 TYR J 22 PHE 0.015 0.002 PHE J 138 TRP 0.025 0.002 TRP D 21 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (17049) covalent geometry : angle 0.64848 / 0.34 (23061) SS BOND : bond 0.00598 / 0.39 ( 24) SS BOND : angle 2.63637 / 1.60 ( 48) hydrogen bonds : bond 0.05092 / 3.34 ( 663) hydrogen bonds : angle 6.10314 / 4.32 ( 1737) link_NAG-ASN : bond 0.00261 / 0.19 ( 9) link_NAG-ASN : angle 2.74201 / 1.63 ( 27) *********************** 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 289 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6714 (ttp) REVERT: D 117 LYS cc_start: 0.7765 (ptpp) cc_final: 0.7551 (ptpp) REVERT: G 70 GLU cc_start: 0.5106 (tm-30) cc_final: 0.4871 (pp20) REVERT: G 105 GLU cc_start: 0.6986 (mp0) cc_final: 0.6193 (mp0) REVERT: J 115 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6839 (ttp) REVERT: L 70 GLU cc_start: 0.5322 (OUTLIER) cc_final: 0.5015 (pp20) outliers start: 53 outliers final: 33 residues processed: 255 average time/residue: 0.1263 time to fit residues: 50.3031 Evaluate side-chains 241 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 88 MET Chi-restraints excluded: chain C residue 119 TYR 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 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 115 MET 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 11 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 41 LYS 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 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 L residue 37 GLU Chi-restraints excluded: chain L residue 70 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.0050 chunk 200 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 44 optimal weight: 0.0570 overall best weight: 0.7316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 6 GLN K 6 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.152070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126198 restraints weight = 36176.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127723 restraints weight = 22458.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.129024 restraints weight = 16241.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129133 restraints weight = 13335.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129489 restraints weight = 12593.166| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17082 Z= 0.123 Angle : 0.618 8.621 23136 Z= 0.320 Chirality : 0.042 0.196 2517 Planarity : 0.004 0.042 3009 Dihedral : 5.175 29.938 2304 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.53 % Allowed : 13.89 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2097 helix: 1.00 (0.27), residues: 321 sheet: 0.31 (0.22), residues: 498 loop : -0.98 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 54 TYR 0.016 0.001 TYR J 22 PHE 0.016 0.001 PHE J 138 TRP 0.024 0.002 TRP D 21 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17049) covalent geometry : angle 0.60225 / 0.31 (23061) SS BOND : bond 0.00570 / 0.35 ( 24) SS BOND : angle 2.56396 / 1.55 ( 48) hydrogen bonds : bond 0.04637 / 3.04 ( 663) hydrogen bonds : angle 5.90939 / 4.19 ( 1737) link_NAG-ASN : bond 0.00227 / 0.16 ( 9) link_NAG-ASN : angle 2.38617 / 1.40 ( 27) *********************** 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 278 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7229 (ptp) cc_final: 0.6964 (ptp) REVERT: C 106 HIS cc_start: 0.7799 (m-70) cc_final: 0.7578 (m90) REVERT: D 102 MET cc_start: 0.8823 (mtp) cc_final: 0.8611 (mtp) REVERT: D 115 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6775 (ttp) REVERT: D 128 GLU cc_start: 0.5629 (mp0) cc_final: 0.5383 (tp30) REVERT: D 149 MET cc_start: 0.3270 (tpt) cc_final: 0.2721 (ptt) REVERT: G 70 GLU cc_start: 0.5418 (tm-30) cc_final: 0.5125 (pp20) REVERT: G 105 GLU cc_start: 0.6996 (mp0) cc_final: 0.6183 (mp0) REVERT: J 115 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7040 (ttp) REVERT: J 128 GLU cc_start: 0.5835 (mp0) cc_final: 0.5414 (tp30) REVERT: K 46 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6928 (pt0) outliers start: 46 outliers final: 24 residues processed: 252 average time/residue: 0.1229 time to fit residues: 48.1424 Evaluate side-chains 228 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 88 MET Chi-restraints excluded: chain C residue 119 TYR 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 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 100 ASP 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 H residue 339 VAL 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 100 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 203 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN K 6 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.145181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120025 restraints weight = 37030.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120358 restraints weight = 26564.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121075 restraints weight = 21460.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.121532 restraints weight = 17112.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.121604 restraints weight = 14996.498| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17082 Z= 0.187 Angle : 0.665 8.735 23136 Z= 0.346 Chirality : 0.044 0.210 2517 Planarity : 0.004 0.040 3009 Dihedral : 5.254 26.222 2304 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.02 % Allowed : 13.89 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2097 helix: 1.07 (0.27), residues: 318 sheet: 0.06 (0.22), residues: 483 loop : -1.07 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 54 TYR 0.015 0.002 TYR E 32 PHE 0.021 0.002 PHE H 141 TRP 0.026 0.002 TRP C 21 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (17049) covalent geometry : angle 0.64884 / 0.34 (23061) SS BOND : bond 0.00649 / 0.41 ( 24) SS BOND : angle 2.54919 / 1.53 ( 48) hydrogen bonds : bond 0.04796 / 3.15 ( 663) hydrogen bonds : angle 5.91699 / 4.19 ( 1737) link_NAG-ASN : bond 0.00247 / 0.17 ( 9) link_NAG-ASN : angle 2.69425 / 1.63 ( 27) *********************** 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 268 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6815 (ttp) REVERT: D 128 GLU cc_start: 0.5671 (mp0) cc_final: 0.5308 (tp30) REVERT: D 149 MET cc_start: 0.3297 (tpt) cc_final: 0.2792 (ppp) REVERT: G 70 GLU cc_start: 0.5606 (tm-30) cc_final: 0.5281 (pp20) REVERT: G 100 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6651 (pt0) REVERT: G 105 GLU cc_start: 0.7113 (mp0) cc_final: 0.6709 (mp0) REVERT: H 139 MET cc_start: 0.7433 (ttm) cc_final: 0.7088 (ttm) REVERT: J 115 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7043 (ttp) REVERT: K 46 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6976 (pt0) outliers start: 55 outliers final: 38 residues processed: 238 average time/residue: 0.1236 time to fit residues: 46.3183 Evaluate side-chains 243 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 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 80 MET 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 258 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR 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 G residue 100 GLN 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 H residue 339 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 103 GLU 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 L residue 37 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 18 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 163 optimal weight: 0.3980 chunk 65 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.149731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124109 restraints weight = 36749.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125519 restraints weight = 23895.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126306 restraints weight = 18346.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126514 restraints weight = 15252.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126515 restraints weight = 14065.397| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17082 Z= 0.167 Angle : 0.639 11.358 23136 Z= 0.331 Chirality : 0.043 0.202 2517 Planarity : 0.004 0.043 3009 Dihedral : 5.190 24.659 2304 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.35 % Allowed : 13.40 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2097 helix: 1.12 (0.27), residues: 318 sheet: 0.15 (0.23), residues: 459 loop : -1.13 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 54 TYR 0.017 0.001 TYR E 32 PHE 0.018 0.002 PHE A 298 TRP 0.020 0.002 TRP C 21 HIS 0.005 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (17049) covalent geometry : angle 0.62405 / 0.33 (23061) SS BOND : bond 0.00584 / 0.36 ( 24) SS BOND : angle 2.48263 / 1.51 ( 48) hydrogen bonds : bond 0.04608 / 3.02 ( 663) hydrogen bonds : angle 5.83503 / 4.13 ( 1737) link_NAG-ASN : bond 0.00250 / 0.17 ( 9) link_NAG-ASN : angle 2.41119 / 1.47 ( 27) *********************** 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 280 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8232 (mtm) REVERT: I 55 GLN cc_start: 0.6387 (tp40) cc_final: 0.5531 (tt0) REVERT: I 105 GLU cc_start: 0.7140 (mp0) cc_final: 0.6917 (mp0) REVERT: D 115 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6734 (ttp) REVERT: H 139 MET cc_start: 0.7424 (ttm) cc_final: 0.7175 (ttm) REVERT: J 115 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6899 (ttp) REVERT: K 46 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6970 (pt0) outliers start: 61 outliers final: 42 residues processed: 246 average time/residue: 0.1163 time to fit residues: 45.6549 Evaluate side-chains 242 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 256 ASN 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 80 MET 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 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 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 48 MET 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 4 MET 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 263 PHE 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 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 L residue 37 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 84 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.147537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121628 restraints weight = 36966.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122957 restraints weight = 25245.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123696 restraints weight = 18979.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123923 restraints weight = 15070.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.124035 restraints weight = 13895.210| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17082 Z= 0.245 Angle : 0.717 10.836 23136 Z= 0.372 Chirality : 0.045 0.242 2517 Planarity : 0.005 0.057 3009 Dihedral : 5.514 23.445 2304 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.68 % Allowed : 13.95 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2097 helix: 0.93 (0.27), residues: 318 sheet: -0.31 (0.23), residues: 483 loop : -1.33 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 54 TYR 0.018 0.002 TYR E 32 PHE 0.017 0.002 PHE C 138 TRP 0.013 0.002 TRP F 47 HIS 0.007 0.002 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.25 (17049) covalent geometry : angle 0.70072 / 0.37 (23061) SS BOND : bond 0.00735 / 0.47 ( 24) SS BOND : angle 2.55419 / 1.56 ( 48) hydrogen bonds : bond 0.04879 / 3.18 ( 663) hydrogen bonds : angle 5.96285 / 4.20 ( 1737) link_NAG-ASN : bond 0.00409 / 0.29 ( 9) link_NAG-ASN : angle 3.10001 / 1.90 ( 27) *********************** 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 280 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7146 (ptp) cc_final: 0.6045 (ppp) REVERT: C 88 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: I 55 GLN cc_start: 0.6348 (tp40) cc_final: 0.6015 (tp40) REVERT: D 115 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6778 (ttp) REVERT: D 149 MET cc_start: 0.3495 (tpt) cc_final: 0.2855 (ppp) REVERT: G 70 GLU cc_start: 0.5995 (tm-30) cc_final: 0.5779 (tm-30) REVERT: G 100 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6778 (pt0) REVERT: G 105 GLU cc_start: 0.7272 (mp0) cc_final: 0.6939 (mp0) REVERT: H 139 MET cc_start: 0.7746 (ttm) cc_final: 0.7528 (ttm) REVERT: J 115 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6962 (ttp) outliers start: 67 outliers final: 46 residues processed: 249 average time/residue: 0.1194 time to fit residues: 47.4979 Evaluate side-chains 251 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 80 MET 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 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 48 MET 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 4 MET 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 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 263 PHE 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 J residue 73 ILE Chi-restraints excluded: chain J residue 103 GLU 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 L residue 37 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 32 optimal weight: 0.0040 chunk 180 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.148834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.123144 restraints weight = 36703.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.124312 restraints weight = 24667.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125110 restraints weight = 18632.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125591 restraints weight = 14622.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.125698 restraints weight = 13711.129| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17082 Z= 0.172 Angle : 0.680 10.262 23136 Z= 0.353 Chirality : 0.045 0.285 2517 Planarity : 0.004 0.063 3009 Dihedral : 5.331 25.224 2304 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.75 % Allowed : 15.71 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2097 helix: 1.13 (0.27), residues: 315 sheet: -0.06 (0.23), residues: 459 loop : -1.31 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 54 TYR 0.021 0.001 TYR D 157 PHE 0.021 0.002 PHE I 71 TRP 0.014 0.001 TRP E 47 HIS 0.007 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (17049) covalent geometry : angle 0.66318 / 0.35 (23061) SS BOND : bond 0.00607 / 0.37 ( 24) SS BOND : angle 2.56620 / 1.57 ( 48) hydrogen bonds : bond 0.04579 / 3.00 ( 663) hydrogen bonds : angle 5.88232 / 4.15 ( 1737) link_NAG-ASN : bond 0.00356 / 0.21 ( 9) link_NAG-ASN : angle 3.06490 / 1.68 ( 27) *********************** 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 266 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7163 (ptp) cc_final: 0.6026 (ppp) REVERT: I 55 GLN cc_start: 0.6325 (tp40) cc_final: 0.5957 (tp40) REVERT: D 115 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6743 (ttp) REVERT: G 11 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6117 (pp) REVERT: G 70 GLU cc_start: 0.6075 (tm-30) cc_final: 0.5851 (tm-30) REVERT: G 105 GLU cc_start: 0.7210 (mp0) cc_final: 0.6875 (mp0) REVERT: H 217 LEU cc_start: 0.8413 (tt) cc_final: 0.8107 (tp) REVERT: J 115 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6946 (ttp) outliers start: 50 outliers final: 41 residues processed: 244 average time/residue: 0.1249 time to fit residues: 47.8911 Evaluate side-chains 253 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 80 MET 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 D residue 67 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 48 MET 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 4 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 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 263 PHE 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 103 GLU Chi-restraints excluded: chain J residue 115 MET Chi-restraints excluded: chain K residue 51 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 0.1980 chunk 154 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.148395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.123288 restraints weight = 36681.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123773 restraints weight = 22610.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124511 restraints weight = 20123.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124989 restraints weight = 15428.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.125038 restraints weight = 14519.394| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17082 Z= 0.191 Angle : 0.700 9.965 23136 Z= 0.364 Chirality : 0.045 0.231 2517 Planarity : 0.005 0.058 3009 Dihedral : 5.353 23.180 2304 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.80 % Allowed : 16.58 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.17), residues: 2097 helix: 1.08 (0.27), residues: 315 sheet: -0.13 (0.23), residues: 474 loop : -1.36 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 54 TYR 0.019 0.002 TYR D 157 PHE 0.020 0.002 PHE A 163 TRP 0.013 0.002 TRP E 47 HIS 0.007 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (17049) covalent geometry : angle 0.68514 / 0.36 (23061) SS BOND : bond 0.00625 / 0.39 ( 24) SS BOND : angle 2.56196 / 1.59 ( 48) hydrogen bonds : bond 0.04634 / 3.05 ( 663) hydrogen bonds : angle 5.92282 / 4.18 ( 1737) link_NAG-ASN : bond 0.00270 / 0.18 ( 9) link_NAG-ASN : angle 2.75212 / 1.52 ( 27) ********************** 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 268 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7144 (ptp) cc_final: 0.6093 (ppp) REVERT: I 55 GLN cc_start: 0.6317 (tp40) cc_final: 0.5962 (tp40) REVERT: D 115 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6628 (ttp) REVERT: D 149 MET cc_start: 0.3350 (tpt) cc_final: 0.2815 (ppp) REVERT: G 70 GLU cc_start: 0.6161 (tm-30) cc_final: 0.5884 (tm-30) REVERT: G 100 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6680 (pt0) REVERT: G 105 GLU cc_start: 0.7244 (mp0) cc_final: 0.6991 (mp0) REVERT: H 112 ILE cc_start: 0.8464 (pp) cc_final: 0.8200 (pt) REVERT: H 180 MET cc_start: 0.8064 (mmm) cc_final: 0.7739 (mtp) REVERT: H 217 LEU cc_start: 0.8399 (tt) cc_final: 0.8098 (tp) REVERT: J 115 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6862 (ttp) outliers start: 51 outliers final: 41 residues processed: 246 average time/residue: 0.1247 time to fit residues: 48.0012 Evaluate side-chains 246 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 80 MET 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 D residue 55 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 263 PHE 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 103 GLU 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 L residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 121 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125720 restraints weight = 36618.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.125719 restraints weight = 25630.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127021 restraints weight = 19945.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127232 restraints weight = 15503.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127288 restraints weight = 14264.716| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17082 Z= 0.137 Angle : 0.680 11.933 23136 Z= 0.353 Chirality : 0.044 0.219 2517 Planarity : 0.004 0.068 3009 Dihedral : 5.156 24.373 2304 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.14 % Allowed : 17.30 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2097 helix: 1.22 (0.28), residues: 315 sheet: -0.06 (0.23), residues: 474 loop : -1.30 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 54 TYR 0.022 0.001 TYR D 157 PHE 0.032 0.002 PHE L 92 TRP 0.016 0.001 TRP E 47 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (17049) covalent geometry : angle 0.66469 / 0.35 (23061) SS BOND : bond 0.00601 / 0.34 ( 24) SS BOND : angle 2.58604 / 1.56 ( 48) hydrogen bonds : bond 0.04362 / 2.88 ( 663) hydrogen bonds : angle 5.85792 / 4.14 ( 1737) link_NAG-ASN : bond 0.00313 / 0.20 ( 9) link_NAG-ASN : angle 2.54600 / 1.40 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.08 seconds wall clock time: 44 minutes 57.51 seconds (2697.51 seconds total)