Starting phenix.real_space_refine on Wed Mar 4 21:54:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mlm_9139/03_2026/6mlm_9139.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mlm_9139/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6mlm_9139/03_2026/6mlm_9139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mlm_9139/03_2026/6mlm_9139.map" model { file = "/net/cci-nas-00/data/ceres_data/6mlm_9139/03_2026/6mlm_9139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mlm_9139/03_2026/6mlm_9139.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, H, D, J, F, K, G, L Time building chain proxies: 2.98, per 1000 atoms: 0.18 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: 1.27 Conformation dependent library (CDL) restraints added in 678.0 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: 0.53 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: 2.84 Time building geometry restraints manager: 1.72 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: 9869 17.65 - 35.30: 316 35.30 - 52.96: 69 52.96 - 70.61: 57 70.61 - 88.26: 21 Dihedral angle restraints: 10332 sinusoidal: 4284 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 10329 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: 0.02 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: 1.030 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.145 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 : 11.419 88.259 6402 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 covalent geometry : bond 0.01321 (17049) covalent geometry : angle 1.31031 (23061) SS BOND : bond 0.04934 ( 24) SS BOND : angle 7.86537 ( 48) hydrogen bonds : bond 0.17918 ( 663) hydrogen bonds : angle 7.95945 ( 1737) link_NAG-ASN : bond 0.06533 ( 9) link_NAG-ASN : angle 3.75946 ( 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 : 0.604 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: 0.1568 time to fit residues: 112.1278 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 : 0.705 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4200 r_free = 0.4200 target = 0.153185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127346 restraints weight = 36433.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.129977 restraints weight = 21879.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.130337 restraints weight = 14733.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.131170 restraints weight = 12837.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131346 restraints weight = 11195.080| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17082 Z= 0.181 Angle : 0.753 12.457 23136 Z= 0.394 Chirality : 0.045 0.269 2517 Planarity : 0.005 0.045 3009 Dihedral : 6.361 64.793 2495 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.75 % Allowed : 7.36 % Favored : 89.90 % 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: 0.18 (0.18), residues: 2097 helix: 1.21 (0.27), residues: 333 sheet: 0.65 (0.21), residues: 576 loop : -0.44 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 54 TYR 0.021 0.002 TYR D 119 PHE 0.028 0.002 PHE D 138 TRP 0.011 0.001 TRP D 14 HIS 0.006 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00396 (17049) covalent geometry : angle 0.72641 (23061) SS BOND : bond 0.00486 ( 24) SS BOND : angle 2.99942 ( 48) hydrogen bonds : bond 0.06281 ( 663) hydrogen bonds : angle 6.57442 ( 1737) link_NAG-ASN : bond 0.00410 ( 9) link_NAG-ASN : angle 4.35103 ( 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 355 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.6604 (p) cc_final: 0.5494 (p) REVERT: C 149 MET cc_start: 0.4239 (tpt) cc_final: 0.3489 (ptt) REVERT: B 69 THR cc_start: 0.6796 (p) cc_final: 0.5156 (p) REVERT: D 61 GLN cc_start: 0.5771 (OUTLIER) cc_final: 0.5482 (mm110) REVERT: D 149 MET cc_start: 0.4144 (tpt) cc_final: 0.3683 (ptt) REVERT: H 69 THR cc_start: 0.6706 (p) cc_final: 0.5439 (p) REVERT: J 149 MET cc_start: 0.4570 (tpt) cc_final: 0.4087 (ptt) outliers start: 50 outliers final: 22 residues processed: 328 average time/residue: 0.1318 time to fit residues: 64.8879 Evaluate side-chains 252 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain 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: 6.9990 chunk 172 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN ** 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 = 0.4110 r_free = 0.4110 target = 0.147793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.122251 restraints weight = 37195.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.122784 restraints weight = 24043.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123385 restraints weight = 20369.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123821 restraints weight = 16644.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123900 restraints weight = 15293.508| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17082 Z= 0.288 Angle : 0.796 10.945 23136 Z= 0.417 Chirality : 0.046 0.208 2517 Planarity : 0.005 0.046 3009 Dihedral : 6.485 60.569 2493 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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: -0.67 (0.17), residues: 2097 helix: 0.87 (0.27), residues: 321 sheet: 0.05 (0.20), residues: 537 loop : -1.04 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 54 TYR 0.022 0.003 TYR I 49 PHE 0.028 0.003 PHE L 71 TRP 0.031 0.003 TRP C 21 HIS 0.007 0.002 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00644 (17049) covalent geometry : angle 0.77859 (23061) SS BOND : bond 0.01290 ( 24) SS BOND : angle 2.57097 ( 48) hydrogen bonds : bond 0.05953 ( 663) hydrogen bonds : angle 6.34448 ( 1737) link_NAG-ASN : bond 0.00511 ( 9) link_NAG-ASN : angle 3.66145 ( 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 318 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 246 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 GLU cc_start: 0.2268 (mt-10) cc_final: 0.1734 (mt-10) REVERT: C 22 TYR cc_start: 0.8227 (m-80) cc_final: 0.7878 (m-80) REVERT: C 149 MET cc_start: 0.4351 (tpt) cc_final: 0.4130 (tpt) REVERT: E 96 MET cc_start: 0.6915 (tpt) cc_final: 0.6681 (tpt) REVERT: D 149 MET cc_start: 0.4163 (tpt) cc_final: 0.3916 (ppp) REVERT: F 23 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8598 (mtpp) REVERT: L 70 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.5065 (pp20) outliers start: 72 outliers final: 37 residues processed: 284 average time/residue: 0.1128 time to fit residues: 50.5539 Evaluate side-chains 251 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain 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 258 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain 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 100 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: 0.0010 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.145892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.121958 restraints weight = 36861.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.121683 restraints weight = 23002.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122951 restraints weight = 21611.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123233 restraints weight = 14886.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.123794 restraints weight = 14008.862| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17082 Z= 0.157 Angle : 0.668 10.194 23136 Z= 0.344 Chirality : 0.043 0.186 2517 Planarity : 0.004 0.041 3009 Dihedral : 5.926 53.155 2493 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.91 % Allowed : 12.80 % Favored : 84.29 % 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: -0.62 (0.17), residues: 2097 helix: 0.96 (0.27), residues: 321 sheet: 0.13 (0.21), residues: 528 loop : -1.04 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 54 TYR 0.016 0.001 TYR C 157 PHE 0.016 0.002 PHE F 63 TRP 0.028 0.002 TRP D 21 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00337 (17049) covalent geometry : angle 0.64759 (23061) SS BOND : bond 0.00946 ( 24) SS BOND : angle 2.66805 ( 48) hydrogen bonds : bond 0.05111 ( 663) hydrogen bonds : angle 6.07813 ( 1737) link_NAG-ASN : bond 0.00176 ( 9) link_NAG-ASN : angle 3.32150 ( 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 283 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 149 MET cc_start: 0.4097 (tpt) cc_final: 0.3726 (ptt) REVERT: G 70 GLU cc_start: 0.5231 (tm-30) cc_final: 0.4980 (pp20) REVERT: G 105 GLU cc_start: 0.7027 (mp0) cc_final: 0.6286 (mp0) REVERT: J 102 MET cc_start: 0.8703 (mtp) cc_final: 0.8477 (mtp) REVERT: L 70 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.5005 (pp20) outliers start: 53 outliers final: 35 residues processed: 250 average time/residue: 0.1145 time to fit residues: 44.9331 Evaluate side-chains 240 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 C residue 67 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP 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 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: 1.9990 chunk 2 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 102 optimal weight: 0.0470 chunk 165 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 126 optimal weight: 0.0770 chunk 97 optimal weight: 0.6980 chunk 115 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.151319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124849 restraints weight = 36135.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127113 restraints weight = 23464.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128721 restraints weight = 15177.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.128552 restraints weight = 12042.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.128931 restraints weight = 11564.104| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17082 Z= 0.126 Angle : 0.630 9.097 23136 Z= 0.324 Chirality : 0.042 0.197 2517 Planarity : 0.004 0.053 3009 Dihedral : 5.486 42.004 2493 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.64 % Allowed : 13.73 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.56 (0.17), residues: 2097 helix: 0.97 (0.27), residues: 321 sheet: 0.26 (0.22), residues: 498 loop : -1.01 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 54 TYR 0.018 0.001 TYR K 32 PHE 0.014 0.001 PHE H 298 TRP 0.019 0.001 TRP J 21 HIS 0.005 0.001 HIS C 26 Details of bonding type rmsd covalent geometry : bond 0.00268 (17049) covalent geometry : angle 0.61036 (23061) SS BOND : bond 0.00554 ( 24) SS BOND : angle 2.58345 ( 48) hydrogen bonds : bond 0.04651 ( 663) hydrogen bonds : angle 5.88891 ( 1737) link_NAG-ASN : bond 0.00225 ( 9) link_NAG-ASN : angle 3.12117 ( 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 283 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7194 (ptp) cc_final: 0.6928 (ptp) REVERT: D 128 GLU cc_start: 0.5539 (mp0) cc_final: 0.5327 (tp30) REVERT: D 149 MET cc_start: 0.4101 (tpt) cc_final: 0.3668 (ptt) REVERT: G 70 GLU cc_start: 0.5375 (tm-30) cc_final: 0.5087 (pp20) REVERT: J 128 GLU cc_start: 0.5837 (mp0) cc_final: 0.5441 (tp30) outliers start: 48 outliers final: 31 residues processed: 255 average time/residue: 0.1200 time to fit residues: 47.0873 Evaluate side-chains 236 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL 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 51 ILE 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 256 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 88 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 203 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.148975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.122923 restraints weight = 36652.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124589 restraints weight = 24188.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125435 restraints weight = 17250.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.125677 restraints weight = 14494.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.125985 restraints weight = 13757.336| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4426 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= 0.194 Angle : 0.676 8.962 23136 Z= 0.351 Chirality : 0.043 0.188 2517 Planarity : 0.005 0.055 3009 Dihedral : 5.563 31.510 2493 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.29 % Allowed : 13.56 % Favored : 83.14 % 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: 0.96 (0.27), residues: 318 sheet: 0.25 (0.23), residues: 453 loop : -1.13 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 54 TYR 0.015 0.002 TYR E 32 PHE 0.020 0.002 PHE L 71 TRP 0.023 0.002 TRP D 21 HIS 0.005 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00432 (17049) covalent geometry : angle 0.65787 (23061) SS BOND : bond 0.00780 ( 24) SS BOND : angle 2.58153 ( 48) hydrogen bonds : bond 0.04824 ( 663) hydrogen bonds : angle 5.91350 ( 1737) link_NAG-ASN : bond 0.00211 ( 9) link_NAG-ASN : angle 3.19260 ( 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 279 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 TYR cc_start: 0.8024 (m-80) cc_final: 0.7765 (m-80) REVERT: D 102 MET cc_start: 0.8906 (mtp) cc_final: 0.8603 (mtp) REVERT: D 117 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7429 (ptpp) REVERT: D 120 GLU cc_start: 0.6936 (pp20) cc_final: 0.6291 (pt0) REVERT: G 70 GLU cc_start: 0.5545 (OUTLIER) cc_final: 0.5299 (pp20) REVERT: G 100 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6642 (pt0) REVERT: G 105 GLU cc_start: 0.7183 (mp0) cc_final: 0.6433 (mp0) REVERT: H 130 ARG cc_start: 0.6681 (ttp-110) cc_final: 0.6471 (ttp-110) REVERT: H 139 MET cc_start: 0.7510 (ttm) cc_final: 0.7054 (ttm) REVERT: K 46 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6945 (pt0) outliers start: 60 outliers final: 45 residues processed: 248 average time/residue: 0.1126 time to fit residues: 43.7194 Evaluate side-chains 246 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 251 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 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 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL 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 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 70 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 329 SER 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 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 4 MET 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: 4.9990 chunk 115 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.148667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.123675 restraints weight = 36695.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123369 restraints weight = 24445.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124392 restraints weight = 20131.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.124743 restraints weight = 15971.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124899 restraints weight = 15114.031| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17082 Z= 0.176 Angle : 0.653 8.784 23136 Z= 0.339 Chirality : 0.043 0.181 2517 Planarity : 0.004 0.043 3009 Dihedral : 5.508 28.646 2493 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.62 % Allowed : 13.89 % Favored : 82.48 % 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: -0.76 (0.17), residues: 2097 helix: 1.01 (0.27), residues: 318 sheet: 0.12 (0.23), residues: 459 loop : -1.17 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 54 TYR 0.016 0.001 TYR E 32 PHE 0.017 0.002 PHE L 71 TRP 0.021 0.002 TRP C 21 HIS 0.005 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00393 (17049) covalent geometry : angle 0.63492 (23061) SS BOND : bond 0.00612 ( 24) SS BOND : angle 2.58058 ( 48) hydrogen bonds : bond 0.04627 ( 663) hydrogen bonds : angle 5.84903 ( 1737) link_NAG-ASN : bond 0.00197 ( 9) link_NAG-ASN : angle 3.07902 ( 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 284 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 105 GLU cc_start: 0.7163 (mp0) cc_final: 0.6959 (mp0) REVERT: D 22 TYR cc_start: 0.8057 (m-80) cc_final: 0.7816 (m-80) REVERT: D 117 LYS cc_start: 0.7587 (ptpp) cc_final: 0.7340 (ptpp) REVERT: D 120 GLU cc_start: 0.6869 (pp20) cc_final: 0.6271 (pt0) REVERT: G 100 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6649 (pt0) REVERT: H 139 MET cc_start: 0.7500 (ttm) cc_final: 0.7056 (ttm) outliers start: 66 outliers final: 50 residues processed: 249 average time/residue: 0.1148 time to fit residues: 45.1824 Evaluate side-chains 243 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 C residue 152 ILE 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 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 256 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain 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 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 263 PHE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 32 TYR 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 4 MET 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: 2.9990 chunk 14 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS K 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120677 restraints weight = 37176.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120419 restraints weight = 24334.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.121506 restraints weight = 22203.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121723 restraints weight = 18498.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121857 restraints weight = 17191.349| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17082 Z= 0.288 Angle : 0.773 9.728 23136 Z= 0.401 Chirality : 0.046 0.262 2517 Planarity : 0.005 0.057 3009 Dihedral : 6.158 34.144 2493 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.73 % Allowed : 14.61 % Favored : 81.66 % 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: -1.16 (0.17), residues: 2097 helix: 0.84 (0.27), residues: 318 sheet: -0.36 (0.23), residues: 480 loop : -1.40 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 54 TYR 0.021 0.002 TYR E 32 PHE 0.026 0.003 PHE H 163 TRP 0.024 0.002 TRP C 21 HIS 0.007 0.002 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00649 (17049) covalent geometry : angle 0.75376 (23061) SS BOND : bond 0.00747 ( 24) SS BOND : angle 2.70899 ( 48) hydrogen bonds : bond 0.05150 ( 663) hydrogen bonds : angle 6.10886 ( 1737) link_NAG-ASN : bond 0.00599 ( 9) link_NAG-ASN : angle 3.70049 ( 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 282 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7252 (ptp) cc_final: 0.6211 (ppp) REVERT: I 55 GLN cc_start: 0.6379 (tp40) cc_final: 0.6064 (tp40) REVERT: D 22 TYR cc_start: 0.8068 (m-80) cc_final: 0.7782 (m-80) REVERT: F 67 VAL cc_start: 0.8917 (p) cc_final: 0.8696 (t) REVERT: G 100 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: G 105 GLU cc_start: 0.7355 (mp0) cc_final: 0.7078 (mp0) REVERT: H 336 MET cc_start: 0.7221 (ptp) cc_final: 0.6380 (ppp) outliers start: 68 outliers final: 52 residues processed: 251 average time/residue: 0.1087 time to fit residues: 43.3607 Evaluate side-chains 243 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 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 256 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain 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 H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 4 MET 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: 1.9990 chunk 76 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 0.0570 chunk 178 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125290 restraints weight = 36790.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124459 restraints weight = 24421.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.125801 restraints weight = 20825.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126171 restraints weight = 15691.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126256 restraints weight = 14877.631| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4925 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= 0.144 Angle : 0.675 9.071 23136 Z= 0.349 Chirality : 0.044 0.222 2517 Planarity : 0.004 0.062 3009 Dihedral : 5.572 28.424 2493 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.86 % Allowed : 16.25 % Favored : 80.89 % 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: -0.90 (0.18), residues: 2097 helix: 1.19 (0.28), residues: 315 sheet: -0.10 (0.23), residues: 474 loop : -1.29 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 54 TYR 0.017 0.001 TYR D 157 PHE 0.021 0.002 PHE I 71 TRP 0.015 0.001 TRP E 47 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00319 (17049) covalent geometry : angle 0.65629 (23061) SS BOND : bond 0.00596 ( 24) SS BOND : angle 2.69299 ( 48) hydrogen bonds : bond 0.04494 ( 663) hydrogen bonds : angle 5.90515 ( 1737) link_NAG-ASN : bond 0.00217 ( 9) link_NAG-ASN : angle 3.16890 ( 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 276 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.7494 (ttm) cc_final: 0.7166 (ttm) REVERT: A 336 MET cc_start: 0.7307 (ptp) cc_final: 0.6209 (ppp) REVERT: C 22 TYR cc_start: 0.7993 (m-80) cc_final: 0.7575 (m-80) REVERT: I 55 GLN cc_start: 0.6290 (tp40) cc_final: 0.5927 (tp40) REVERT: D 117 LYS cc_start: 0.7645 (ptpp) cc_final: 0.7390 (ptpp) REVERT: D 120 GLU cc_start: 0.6930 (pp20) cc_final: 0.6386 (pt0) REVERT: F 69 MET cc_start: 0.7735 (mtp) cc_final: 0.7473 (mtp) REVERT: G 11 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6161 (pp) REVERT: G 70 GLU cc_start: 0.6079 (tm-30) cc_final: 0.5844 (tm-30) REVERT: G 100 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6698 (pt0) REVERT: G 105 GLU cc_start: 0.7217 (mp0) cc_final: 0.6935 (mp0) REVERT: H 139 MET cc_start: 0.7369 (ttm) cc_final: 0.7167 (ttm) REVERT: H 217 LEU cc_start: 0.8328 (tt) cc_final: 0.8055 (tp) outliers start: 52 outliers final: 43 residues processed: 254 average time/residue: 0.1153 time to fit residues: 45.8310 Evaluate side-chains 254 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 48 ILE 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 C residue 152 ILE 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 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 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 70 THR 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 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 H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 10.0000 chunk 154 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 101 optimal weight: 0.0000 chunk 163 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.151464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126161 restraints weight = 36838.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.126573 restraints weight = 24156.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127634 restraints weight = 18661.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127913 restraints weight = 15725.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127997 restraints weight = 14659.051| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17082 Z= 0.131 Angle : 0.663 9.572 23136 Z= 0.343 Chirality : 0.043 0.211 2517 Planarity : 0.004 0.062 3009 Dihedral : 5.293 24.257 2493 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.36 % Allowed : 17.52 % Favored : 80.12 % 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: -0.82 (0.18), residues: 2097 helix: 1.28 (0.28), residues: 318 sheet: -0.03 (0.23), residues: 474 loop : -1.26 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 54 TYR 0.022 0.001 TYR D 157 PHE 0.018 0.002 PHE I 71 TRP 0.020 0.001 TRP K 47 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00292 (17049) covalent geometry : angle 0.64505 (23061) SS BOND : bond 0.00688 ( 24) SS BOND : angle 2.66659 ( 48) hydrogen bonds : bond 0.04286 ( 663) hydrogen bonds : angle 5.84600 ( 1737) link_NAG-ASN : bond 0.00288 ( 9) link_NAG-ASN : angle 2.95879 ( 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 264 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7244 (ptp) cc_final: 0.6067 (ppp) REVERT: C 22 TYR cc_start: 0.7623 (m-80) cc_final: 0.7231 (m-80) REVERT: I 55 GLN cc_start: 0.6383 (tp40) cc_final: 0.6033 (tp40) REVERT: B 139 MET cc_start: 0.7362 (ttm) cc_final: 0.7129 (ttm) REVERT: D 117 LYS cc_start: 0.7703 (ptpp) cc_final: 0.7310 (ptpp) REVERT: D 120 GLU cc_start: 0.7016 (pp20) cc_final: 0.6463 (pt0) REVERT: D 149 MET cc_start: 0.3276 (tpt) cc_final: 0.2689 (ptt) REVERT: F 69 MET cc_start: 0.7695 (mtp) cc_final: 0.7410 (mtp) REVERT: G 100 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6592 (pt0) REVERT: G 105 GLU cc_start: 0.7203 (mp0) cc_final: 0.6923 (mp0) REVERT: H 217 LEU cc_start: 0.8253 (tt) cc_final: 0.7985 (tp) REVERT: J 149 MET cc_start: 0.4204 (tpt) cc_final: 0.3894 (tpt) outliers start: 43 outliers final: 38 residues processed: 246 average time/residue: 0.1188 time to fit residues: 45.3702 Evaluate side-chains 240 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 C residue 152 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 ASP 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 H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 121 optimal weight: 6.9990 chunk 202 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 191 optimal weight: 0.0170 chunk 131 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** 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 = 0.4168 r_free = 0.4168 target = 0.153087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127932 restraints weight = 36864.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.128259 restraints weight = 24957.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.129164 restraints weight = 19446.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129576 restraints weight = 15761.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.129700 restraints weight = 14404.653| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5100 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= 0.122 Angle : 0.666 10.340 23136 Z= 0.344 Chirality : 0.043 0.270 2517 Planarity : 0.005 0.062 3009 Dihedral : 5.198 29.036 2493 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.14 % Allowed : 17.41 % Favored : 80.45 % 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: -0.74 (0.18), residues: 2097 helix: 1.41 (0.29), residues: 318 sheet: 0.10 (0.24), residues: 468 loop : -1.26 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 54 TYR 0.025 0.001 TYR K 32 PHE 0.024 0.002 PHE E 63 TRP 0.015 0.001 TRP K 47 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00266 (17049) covalent geometry : angle 0.64601 (23061) SS BOND : bond 0.00570 ( 24) SS BOND : angle 2.66865 ( 48) hydrogen bonds : bond 0.04081 ( 663) hydrogen bonds : angle 5.77417 ( 1737) link_NAG-ASN : bond 0.00813 ( 9) link_NAG-ASN : angle 3.25088 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2427.46 seconds wall clock time: 42 minutes 54.48 seconds (2574.48 seconds total)