Starting phenix.real_space_refine on Thu Feb 5 04:24:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mq7_48515/02_2026/9mq7_48515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mq7_48515/02_2026/9mq7_48515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mq7_48515/02_2026/9mq7_48515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mq7_48515/02_2026/9mq7_48515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mq7_48515/02_2026/9mq7_48515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mq7_48515/02_2026/9mq7_48515.map" } resolution = 3.63 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= 0.023 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 75 5.16 5 C 9255 2.51 5 N 2526 2.21 5 O 2769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14625 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 919 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 919 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 919 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "N" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2503 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "C" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2503 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "E" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2503 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "B" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 645 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "D" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 645 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "F" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 645 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Time building chain proxies: 3.10, per 1000 atoms: 0.21 Number of scatterers: 14625 At special positions: 0 Unit cell: (152, 138, 131, 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 75 16.00 O 2769 8.00 N 2526 7.00 C 9255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.02 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " 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 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 361.6 milliseconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3444 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 41 sheets defined 17.2% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 97 through 100A Processing helix chain 'I' and resid 97 through 100A Processing helix chain 'J' and resid 82B through 85 Processing helix chain 'J' and resid 97 through 100A Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.773A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.812A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.713A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.677A pdb=" N PHE E 79 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 80' Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.650A pdb=" N LEU E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.669A pdb=" N TRP E 127 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'B' and resid 47 through 58 removed outlier: 3.813A pdb=" N ILE B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 120 removed outlier: 4.201A pdb=" N ASP B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 54 through 57 Processing helix chain 'D' and resid 72 through 122 removed outlier: 3.574A pdb=" N GLU D 83 " --> pdb=" O ASN D 79 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL D 113 " --> pdb=" O HIS D 109 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 114 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 58 removed outlier: 4.279A pdb=" N ILE F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 122 removed outlier: 3.504A pdb=" N GLU F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL F 113 " --> pdb=" O HIS F 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS F 114 " --> pdb=" O ASP F 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP H 35 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.500A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP I 35 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.500A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP I 35 " --> pdb=" O GLU I 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 5 through 7 removed outlier: 4.441A pdb=" N PHE J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.696A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP J 35 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.696A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP J 35 " --> pdb=" O GLU J 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.697A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AB2, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.520A pdb=" N LEU M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.830A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.264A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE M 48 " --> pdb=" O TRP M 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.795A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU N 21 " --> pdb=" O LEU N 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.786A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 45 through 48 removed outlier: 5.836A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE N 48 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN N 38 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.161A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.761A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.601A pdb=" N PHE A 232 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 136 through 141 removed outlier: 5.431A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AC5, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.640A pdb=" N GLN A 211 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 287 through 288 removed outlier: 4.177A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.505A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.185A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AD1, first strand: chain 'C' and resid 136 through 141 removed outlier: 5.453A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AD3, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.557A pdb=" N GLN C 211 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR C 206 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 209 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD5, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.271A pdb=" N GLU E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'E' and resid 51 through 53A removed outlier: 5.708A pdb=" N LEU E 51 " --> pdb=" O GLY E 275 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 279 " --> pdb=" O ASP E 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 59 through 61 Processing sheet with id=AE1, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.742A pdb=" N PHE E 232 " --> pdb=" O SER E 101 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 136 through 141 removed outlier: 5.549A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER E 146 " --> pdb=" O CYS E 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AE4, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.765A pdb=" N GLN E 211 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 281 through 282 removed outlier: 4.634A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE E 288 " --> pdb=" O CYS E 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 483 hydrogen bonds defined for protein. 1239 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: 2.34 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4762 1.34 - 1.47: 3632 1.47 - 1.59: 6468 1.59 - 1.71: 0 1.71 - 1.83: 111 Bond restraints: 14973 Sorted by residual: bond pdb=" CB LYS J 13 " pdb=" CG LYS J 13 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C LYS M 39 " pdb=" N PRO M 40 " ideal model delta sigma weight residual 1.331 1.348 -0.017 1.27e-02 6.20e+03 1.87e+00 bond pdb=" CB LYS H 75 " pdb=" CG LYS H 75 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C PRO N 95 " pdb=" N PRO N 95A" ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.61e+00 ... (remaining 14968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 19934 2.41 - 4.81: 308 4.81 - 7.22: 58 7.22 - 9.63: 17 9.63 - 12.04: 8 Bond angle restraints: 20325 Sorted by residual: angle pdb=" C ASN N 93 " pdb=" N TRP N 94 " pdb=" CA TRP N 94 " ideal model delta sigma weight residual 122.28 116.50 5.78 1.02e+00 9.61e-01 3.21e+01 angle pdb=" CA LYS H 75 " pdb=" CB LYS H 75 " pdb=" CG LYS H 75 " ideal model delta sigma weight residual 114.10 125.41 -11.31 2.00e+00 2.50e-01 3.20e+01 angle pdb=" CA LYS H 73 " pdb=" CB LYS H 73 " pdb=" CG LYS H 73 " ideal model delta sigma weight residual 114.10 123.16 -9.06 2.00e+00 2.50e-01 2.05e+01 angle pdb=" N TRP N 94 " pdb=" CA TRP N 94 " pdb=" C TRP N 94 " ideal model delta sigma weight residual 110.73 117.50 -6.77 1.55e+00 4.16e-01 1.91e+01 angle pdb=" CA MET F 57 " pdb=" CB MET F 57 " pdb=" CG MET F 57 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 ... (remaining 20320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7841 17.88 - 35.77: 871 35.77 - 53.65: 172 53.65 - 71.53: 36 71.53 - 89.42: 20 Dihedral angle restraints: 8940 sinusoidal: 3576 harmonic: 5364 Sorted by residual: dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual -86.00 -23.32 -62.68 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -23.89 -62.11 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual 93.00 152.29 -59.29 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 8937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1397 0.032 - 0.065: 515 0.065 - 0.097: 205 0.097 - 0.130: 106 0.130 - 0.162: 12 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CA ILE N 48 " pdb=" N ILE N 48 " pdb=" C ILE N 48 " pdb=" CB ILE N 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA TRP N 94 " pdb=" N TRP N 94 " pdb=" C TRP N 94 " pdb=" CB TRP N 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 2232 not shown) Planarity restraints: 2607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP N 94 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO N 95 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO N 95 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 95 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET F 57 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C MET F 57 " -0.035 2.00e-02 2.50e+03 pdb=" O MET F 57 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN F 58 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 75 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C LYS H 75 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS H 75 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN H 76 " -0.011 2.00e-02 2.50e+03 ... (remaining 2604 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 405 2.68 - 3.23: 14177 3.23 - 3.79: 21658 3.79 - 4.34: 26978 4.34 - 4.90: 45614 Nonbonded interactions: 108832 Sorted by model distance: nonbonded pdb=" NZ LYS M 39 " pdb=" O PRO M 40 " model vdw 2.120 3.120 nonbonded pdb=" O ASP B 55 " pdb=" ND2 ASN B 58 " model vdw 2.168 3.120 nonbonded pdb=" O HIS B 109 " pdb=" ND2 ASN B 112 " model vdw 2.169 3.120 nonbonded pdb=" OE1 GLN H 5 " pdb=" N GLU H 6 " model vdw 2.183 3.120 nonbonded pdb=" OG SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.221 3.040 ... (remaining 108827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.320 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 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 : 0.004 0.041 14991 Z= 0.161 Angle : 0.785 12.035 20361 Z= 0.401 Chirality : 0.044 0.162 2235 Planarity : 0.005 0.059 2607 Dihedral : 15.731 89.415 5442 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.06 % Allowed : 22.78 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.54 (0.19), residues: 1836 helix: 0.78 (0.34), residues: 252 sheet: -0.39 (0.26), residues: 420 loop : -1.77 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 54 TYR 0.016 0.001 TYR N 49 PHE 0.023 0.001 PHE I 78 TRP 0.011 0.001 TRP A 84 HIS 0.003 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00352 (14973) covalent geometry : angle 0.78191 (20325) SS BOND : bond 0.00488 ( 18) SS BOND : angle 1.82397 ( 36) hydrogen bonds : bond 0.16325 ( 457) hydrogen bonds : angle 6.79935 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 HIS cc_start: 0.6545 (m90) cc_final: 0.6162 (m90) REVERT: J 6 GLU cc_start: 0.7035 (pm20) cc_final: 0.6377 (mp0) REVERT: J 100 TYR cc_start: 0.7696 (m-80) cc_final: 0.7284 (m-80) REVERT: J 102 MET cc_start: 0.4204 (ptp) cc_final: 0.3970 (ptp) REVERT: L 37 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7394 (pp30) REVERT: M 92 TYR cc_start: 0.7408 (t80) cc_final: 0.7122 (t80) REVERT: N 37 GLN cc_start: 0.7376 (tm-30) cc_final: 0.6804 (pp30) REVERT: A 47 HIS cc_start: 0.7786 (p90) cc_final: 0.7394 (p-80) REVERT: A 62 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7024 (mtmt) REVERT: A 75 MET cc_start: 0.7532 (mmp) cc_final: 0.7025 (mtm) REVERT: A 90 ARG cc_start: 0.6556 (tpp-160) cc_final: 0.6007 (tpp-160) REVERT: A 107 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6300 (tm-30) REVERT: A 111 MET cc_start: 0.6517 (tpp) cc_final: 0.6248 (tmm) REVERT: A 165 LYS cc_start: 0.7781 (ttmm) cc_final: 0.6972 (tppt) REVERT: A 212 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7405 (ttm-80) REVERT: A 246 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6352 (tt0) REVERT: A 264 ASP cc_start: 0.7128 (t0) cc_final: 0.6880 (m-30) REVERT: A 280 LYS cc_start: 0.7910 (tppt) cc_final: 0.7406 (mmmm) REVERT: A 292 MET cc_start: 0.7259 (mmm) cc_final: 0.6953 (mmt) REVERT: A 304 GLU cc_start: 0.8048 (pt0) cc_final: 0.7104 (pp20) REVERT: A 313 LYS cc_start: 0.7766 (tptt) cc_final: 0.6978 (tptp) REVERT: C 75 MET cc_start: 0.7369 (mmm) cc_final: 0.7036 (mtm) REVERT: C 111 MET cc_start: 0.6718 (tpp) cc_final: 0.6425 (tmm) REVERT: C 165 LYS cc_start: 0.6933 (ttmm) cc_final: 0.6379 (tppt) REVERT: C 173 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7489 (mpt180) REVERT: C 264 ASP cc_start: 0.7005 (t0) cc_final: 0.6741 (m-30) REVERT: E 40 GLN cc_start: 0.7646 (tp-100) cc_final: 0.6931 (tm-30) REVERT: E 121 ILE cc_start: 0.7393 (mm) cc_final: 0.7083 (mt) REVERT: E 124 LYS cc_start: 0.6742 (tppt) cc_final: 0.6452 (tptt) REVERT: E 212 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7382 (ttm-80) REVERT: E 246 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6472 (tt0) REVERT: E 264 ASP cc_start: 0.6463 (t0) cc_final: 0.6174 (m-30) REVERT: E 266 THR cc_start: 0.7350 (m) cc_final: 0.7031 (p) REVERT: E 280 LYS cc_start: 0.8092 (tppt) cc_final: 0.7877 (mmmt) REVERT: E 292 MET cc_start: 0.7265 (mpp) cc_final: 0.7023 (mpp) REVERT: E 313 LYS cc_start: 0.7938 (tptt) cc_final: 0.7142 (tptp) REVERT: B 51 ASN cc_start: 0.8318 (m-40) cc_final: 0.7720 (p0) REVERT: B 82 MET cc_start: 0.5259 (mmm) cc_final: 0.4710 (mmm) REVERT: D 57 MET cc_start: 0.6770 (ppp) cc_final: 0.6181 (ttm) REVERT: D 108 PHE cc_start: 0.7326 (p90) cc_final: 0.6748 (p90) REVERT: F 103 GLU cc_start: 0.6463 (tp30) cc_final: 0.6176 (tp30) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.1157 time to fit residues: 50.9783 Evaluate side-chains 233 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 96 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN A 250 ASN C 222 GLN E 222 GLN D 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.211598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182324 restraints weight = 20444.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181039 restraints weight = 28255.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.182778 restraints weight = 27397.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.183627 restraints weight = 16988.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.184117 restraints weight = 15059.711| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14991 Z= 0.126 Angle : 0.665 18.389 20361 Z= 0.331 Chirality : 0.044 0.158 2235 Planarity : 0.005 0.073 2607 Dihedral : 4.472 48.986 1994 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.64 % Allowed : 19.63 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.30 (0.19), residues: 1836 helix: 1.47 (0.33), residues: 258 sheet: -0.21 (0.27), residues: 390 loop : -1.74 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 73 TYR 0.027 0.001 TYR C 274 PHE 0.017 0.002 PHE I 91 TRP 0.019 0.001 TRP L 35 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00282 (14973) covalent geometry : angle 0.66157 (20325) SS BOND : bond 0.00471 ( 18) SS BOND : angle 1.63216 ( 36) hydrogen bonds : bond 0.04442 ( 457) hydrogen bonds : angle 5.17176 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: J 100 TYR cc_start: 0.8502 (m-80) cc_final: 0.8261 (m-80) REVERT: L 3 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7940 (m) REVERT: M 46 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5542 (tp) REVERT: N 24 ARG cc_start: 0.6951 (ptp90) cc_final: 0.6491 (mtp-110) REVERT: N 47 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6127 (mp) REVERT: A 107 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6862 (tm-30) REVERT: A 268 MET cc_start: 0.7194 (tpt) cc_final: 0.6514 (tpp) REVERT: A 313 LYS cc_start: 0.8365 (tptt) cc_final: 0.7933 (tptp) REVERT: E 292 MET cc_start: 0.7391 (mpp) cc_final: 0.7093 (mpp) REVERT: E 313 LYS cc_start: 0.8428 (tptt) cc_final: 0.8035 (tptp) REVERT: B 51 ASN cc_start: 0.7882 (m-40) cc_final: 0.7457 (p0) REVERT: B 71 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5502 (mt) REVERT: F 103 GLU cc_start: 0.7343 (tp30) cc_final: 0.6971 (tm-30) outliers start: 59 outliers final: 29 residues processed: 276 average time/residue: 0.1051 time to fit residues: 42.1637 Evaluate side-chains 238 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 0.0670 chunk 164 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 168 optimal weight: 0.0060 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 27 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN E 191 GLN D 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.211452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.182885 restraints weight = 20312.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181185 restraints weight = 31565.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183001 restraints weight = 30258.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.183487 restraints weight = 18278.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.184149 restraints weight = 17764.884| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14991 Z= 0.114 Angle : 0.618 18.462 20361 Z= 0.310 Chirality : 0.044 0.154 2235 Planarity : 0.004 0.079 2607 Dihedral : 4.317 31.254 1992 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.58 % Allowed : 20.31 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.21 (0.19), residues: 1836 helix: 1.58 (0.33), residues: 258 sheet: -0.06 (0.27), residues: 390 loop : -1.73 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.015 0.001 TYR C 274 PHE 0.029 0.002 PHE B 108 TRP 0.014 0.001 TRP N 35 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00248 (14973) covalent geometry : angle 0.61257 (20325) SS BOND : bond 0.00510 ( 18) SS BOND : angle 2.03844 ( 36) hydrogen bonds : bond 0.04095 ( 457) hydrogen bonds : angle 4.93365 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: J 100 TYR cc_start: 0.8500 (m-80) cc_final: 0.8244 (m-80) REVERT: L 3 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7914 (m) REVERT: M 46 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5881 (tp) REVERT: M 86 TYR cc_start: 0.7203 (m-80) cc_final: 0.6995 (m-80) REVERT: N 4 MET cc_start: 0.6385 (mmt) cc_final: 0.6116 (mmt) REVERT: N 24 ARG cc_start: 0.6966 (ptp90) cc_final: 0.6632 (mtp180) REVERT: N 47 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6084 (mp) REVERT: A 277 CYS cc_start: 0.2493 (OUTLIER) cc_final: 0.1943 (m) REVERT: A 313 LYS cc_start: 0.8324 (tptt) cc_final: 0.7944 (tptp) REVERT: C 28 THR cc_start: 0.7078 (t) cc_final: 0.6858 (m) REVERT: C 308 TYR cc_start: 0.8641 (t80) cc_final: 0.8309 (t80) REVERT: E 174 GLU cc_start: 0.7231 (pm20) cc_final: 0.6908 (pm20) REVERT: E 292 MET cc_start: 0.7341 (mpp) cc_final: 0.7120 (mmt) REVERT: E 313 LYS cc_start: 0.8489 (tptt) cc_final: 0.8017 (tptp) REVERT: B 51 ASN cc_start: 0.7811 (m-40) cc_final: 0.7491 (p0) REVERT: F 53 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7531 (tp) REVERT: F 56 LYS cc_start: 0.7243 (tptt) cc_final: 0.7012 (tptt) REVERT: F 103 GLU cc_start: 0.7280 (tp30) cc_final: 0.7027 (tm-30) outliers start: 58 outliers final: 33 residues processed: 269 average time/residue: 0.1053 time to fit residues: 42.3346 Evaluate side-chains 246 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN B 112 ASN D 109 HIS ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.207899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178297 restraints weight = 20385.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.177031 restraints weight = 29879.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178614 restraints weight = 29078.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179278 restraints weight = 18818.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179707 restraints weight = 16596.504| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14991 Z= 0.131 Angle : 0.634 17.931 20361 Z= 0.317 Chirality : 0.044 0.159 2235 Planarity : 0.005 0.083 2607 Dihedral : 4.437 30.403 1992 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.63 % Allowed : 20.37 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.33 (0.19), residues: 1836 helix: 1.41 (0.32), residues: 261 sheet: -0.33 (0.27), residues: 390 loop : -1.71 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 45 TYR 0.015 0.001 TYR N 49 PHE 0.028 0.002 PHE B 108 TRP 0.013 0.001 TRP A 84 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00299 (14973) covalent geometry : angle 0.62954 (20325) SS BOND : bond 0.00446 ( 18) SS BOND : angle 1.94191 ( 36) hydrogen bonds : bond 0.04232 ( 457) hydrogen bonds : angle 4.93276 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 212 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: J 100 TYR cc_start: 0.8555 (m-80) cc_final: 0.8255 (m-80) REVERT: L 3 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7947 (m) REVERT: M 37 GLN cc_start: 0.7764 (pp30) cc_final: 0.7340 (pp30) REVERT: M 46 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5838 (tp) REVERT: N 4 MET cc_start: 0.6291 (mmt) cc_final: 0.5960 (mmt) REVERT: N 24 ARG cc_start: 0.7031 (ptp90) cc_final: 0.6661 (mtp180) REVERT: N 47 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6170 (mp) REVERT: A 308 TYR cc_start: 0.8542 (t80) cc_final: 0.8223 (t80) REVERT: A 313 LYS cc_start: 0.8323 (tptt) cc_final: 0.7928 (tptp) REVERT: E 313 LYS cc_start: 0.8506 (tptt) cc_final: 0.7996 (tptp) REVERT: B 51 ASN cc_start: 0.7871 (m-40) cc_final: 0.7551 (p0) REVERT: B 71 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5660 (mt) REVERT: F 103 GLU cc_start: 0.7378 (tp30) cc_final: 0.7023 (tm-30) outliers start: 75 outliers final: 48 residues processed: 267 average time/residue: 0.1153 time to fit residues: 46.1970 Evaluate side-chains 251 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 124 optimal weight: 0.0670 chunk 179 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN N 37 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 222 GLN A 282 GLN E 186 ASN D 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.209395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177813 restraints weight = 20320.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175299 restraints weight = 27675.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.177285 restraints weight = 25297.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178008 restraints weight = 16627.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179796 restraints weight = 14150.368| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14991 Z= 0.136 Angle : 0.651 19.220 20361 Z= 0.324 Chirality : 0.044 0.205 2235 Planarity : 0.005 0.090 2607 Dihedral : 4.492 30.988 1992 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.63 % Allowed : 21.17 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.36 (0.19), residues: 1836 helix: 1.34 (0.32), residues: 261 sheet: -0.43 (0.28), residues: 360 loop : -1.66 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 74 TYR 0.014 0.001 TYR J 52 PHE 0.028 0.002 PHE B 108 TRP 0.013 0.001 TRP A 84 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00318 (14973) covalent geometry : angle 0.64351 (20325) SS BOND : bond 0.00506 ( 18) SS BOND : angle 2.47229 ( 36) hydrogen bonds : bond 0.04244 ( 457) hydrogen bonds : angle 4.93506 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 211 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: J 6 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: J 100 TYR cc_start: 0.8580 (m-80) cc_final: 0.8250 (m-80) REVERT: L 3 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8008 (m) REVERT: N 4 MET cc_start: 0.6346 (mmt) cc_final: 0.6038 (mmt) REVERT: N 24 ARG cc_start: 0.7081 (ptp90) cc_final: 0.6752 (mtp180) REVERT: N 47 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6163 (mp) REVERT: A 313 LYS cc_start: 0.8292 (tptt) cc_final: 0.7931 (tptp) REVERT: E 28 THR cc_start: 0.7512 (t) cc_final: 0.7222 (m) REVERT: E 313 LYS cc_start: 0.8490 (tptt) cc_final: 0.7974 (tptp) REVERT: B 51 ASN cc_start: 0.7930 (m-40) cc_final: 0.7649 (p0) REVERT: B 71 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5621 (mt) REVERT: F 103 GLU cc_start: 0.7304 (tp30) cc_final: 0.6952 (tm-30) outliers start: 75 outliers final: 55 residues processed: 264 average time/residue: 0.1097 time to fit residues: 43.2530 Evaluate side-chains 258 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 29 optimal weight: 2.9990 chunk 143 optimal weight: 0.0970 chunk 148 optimal weight: 0.1980 chunk 81 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.211710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180053 restraints weight = 20524.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.177192 restraints weight = 25874.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.179178 restraints weight = 24601.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.180010 restraints weight = 16090.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.181878 restraints weight = 13490.411| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14991 Z= 0.110 Angle : 0.617 19.882 20361 Z= 0.304 Chirality : 0.043 0.153 2235 Planarity : 0.005 0.092 2607 Dihedral : 4.222 28.772 1992 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.26 % Allowed : 21.98 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.28 (0.19), residues: 1836 helix: 1.41 (0.32), residues: 261 sheet: -0.40 (0.29), residues: 354 loop : -1.60 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 45 TYR 0.016 0.001 TYR C 274 PHE 0.029 0.001 PHE B 108 TRP 0.015 0.001 TRP L 35 HIS 0.004 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00246 (14973) covalent geometry : angle 0.61209 (20325) SS BOND : bond 0.00418 ( 18) SS BOND : angle 2.01148 ( 36) hydrogen bonds : bond 0.03844 ( 457) hydrogen bonds : angle 4.78969 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: H 109 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7365 (t) REVERT: J 6 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: L 3 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8027 (m) REVERT: M 46 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5937 (tp) REVERT: N 4 MET cc_start: 0.6439 (mmt) cc_final: 0.6121 (mmt) REVERT: N 24 ARG cc_start: 0.7067 (ptp90) cc_final: 0.6685 (mtp180) REVERT: N 27 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: N 47 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6094 (mp) REVERT: A 313 LYS cc_start: 0.8300 (tptt) cc_final: 0.7905 (tptp) REVERT: E 292 MET cc_start: 0.7189 (mmt) cc_final: 0.6739 (mmt) REVERT: E 313 LYS cc_start: 0.8472 (tptt) cc_final: 0.7948 (tptp) REVERT: B 51 ASN cc_start: 0.7932 (m-40) cc_final: 0.7625 (p0) REVERT: D 103 GLU cc_start: 0.7209 (tp30) cc_final: 0.6676 (tm-30) REVERT: F 103 GLU cc_start: 0.7248 (tp30) cc_final: 0.6906 (tm-30) outliers start: 69 outliers final: 51 residues processed: 256 average time/residue: 0.1228 time to fit residues: 46.6166 Evaluate side-chains 247 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 126 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 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 = 0.4297 r_free = 0.4297 target = 0.203047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173403 restraints weight = 20299.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171898 restraints weight = 28885.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173358 restraints weight = 29219.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173743 restraints weight = 18383.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174231 restraints weight = 16673.568| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14991 Z= 0.148 Angle : 0.647 19.278 20361 Z= 0.324 Chirality : 0.044 0.163 2235 Planarity : 0.005 0.098 2607 Dihedral : 4.505 26.701 1992 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.75 % Allowed : 22.28 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.39 (0.19), residues: 1836 helix: 1.19 (0.32), residues: 261 sheet: -0.48 (0.27), residues: 387 loop : -1.66 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 45 TYR 0.016 0.001 TYR J 52 PHE 0.027 0.002 PHE B 108 TRP 0.020 0.002 TRP N 35 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00348 (14973) covalent geometry : angle 0.64330 (20325) SS BOND : bond 0.00551 ( 18) SS BOND : angle 1.74486 ( 36) hydrogen bonds : bond 0.04353 ( 457) hydrogen bonds : angle 4.96217 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 202 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: H 25 SER cc_start: 0.5964 (t) cc_final: 0.5677 (p) REVERT: H 109 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7556 (t) REVERT: M 46 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6026 (tp) REVERT: N 24 ARG cc_start: 0.7103 (ptp90) cc_final: 0.6816 (mtp180) REVERT: N 47 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5987 (mp) REVERT: A 150 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.6981 (m-40) REVERT: A 313 LYS cc_start: 0.8330 (tptt) cc_final: 0.7924 (tptp) REVERT: E 28 THR cc_start: 0.7562 (t) cc_final: 0.7309 (m) REVERT: E 292 MET cc_start: 0.7277 (mmt) cc_final: 0.6833 (mmt) REVERT: E 313 LYS cc_start: 0.8490 (tptt) cc_final: 0.7961 (tptp) REVERT: B 71 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5798 (mt) REVERT: D 103 GLU cc_start: 0.7224 (tp30) cc_final: 0.6786 (tm-30) REVERT: F 87 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7655 (mt) REVERT: F 103 GLU cc_start: 0.7271 (tp30) cc_final: 0.6948 (tm-30) outliers start: 77 outliers final: 56 residues processed: 261 average time/residue: 0.1235 time to fit residues: 48.0756 Evaluate side-chains 255 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN E 222 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.204564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.173953 restraints weight = 20446.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173551 restraints weight = 27847.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174898 restraints weight = 28435.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175478 restraints weight = 18365.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175977 restraints weight = 16123.003| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14991 Z= 0.122 Angle : 0.638 18.362 20361 Z= 0.318 Chirality : 0.043 0.155 2235 Planarity : 0.005 0.101 2607 Dihedral : 4.388 29.823 1992 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.57 % Allowed : 22.78 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.30 (0.19), residues: 1836 helix: 1.20 (0.32), residues: 261 sheet: -0.06 (0.30), residues: 324 loop : -1.66 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 114 TYR 0.012 0.001 TYR A 308 PHE 0.028 0.002 PHE B 108 TRP 0.018 0.001 TRP N 35 HIS 0.003 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00280 (14973) covalent geometry : angle 0.62800 (20325) SS BOND : bond 0.00484 ( 18) SS BOND : angle 2.79736 ( 36) hydrogen bonds : bond 0.04028 ( 457) hydrogen bonds : angle 4.87560 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 199 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: H 25 SER cc_start: 0.6006 (t) cc_final: 0.5716 (p) REVERT: L 3 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7932 (m) REVERT: M 46 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6033 (tp) REVERT: N 4 MET cc_start: 0.6681 (mmt) cc_final: 0.6117 (mmt) REVERT: N 24 ARG cc_start: 0.7041 (ptp90) cc_final: 0.6714 (mtp180) REVERT: N 27 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: N 36 TYR cc_start: 0.6101 (m-80) cc_final: 0.5803 (m-80) REVERT: N 47 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5919 (mp) REVERT: A 150 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7046 (m-40) REVERT: A 313 LYS cc_start: 0.8305 (tptt) cc_final: 0.7963 (tptp) REVERT: E 28 THR cc_start: 0.7494 (t) cc_final: 0.7208 (m) REVERT: E 292 MET cc_start: 0.7193 (mmt) cc_final: 0.6758 (mmt) REVERT: E 313 LYS cc_start: 0.8491 (tptt) cc_final: 0.7933 (tptp) REVERT: B 71 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5645 (mt) REVERT: D 103 GLU cc_start: 0.7230 (tp30) cc_final: 0.6766 (tm-30) REVERT: F 103 GLU cc_start: 0.7312 (tp30) cc_final: 0.6892 (tm-30) outliers start: 74 outliers final: 57 residues processed: 256 average time/residue: 0.1051 time to fit residues: 39.8908 Evaluate side-chains 254 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 108 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 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 = 0.4309 r_free = 0.4309 target = 0.203994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.173590 restraints weight = 20554.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172484 restraints weight = 27281.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173965 restraints weight = 28958.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174510 restraints weight = 17858.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175156 restraints weight = 15895.224| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14991 Z= 0.131 Angle : 0.659 18.160 20361 Z= 0.327 Chirality : 0.044 0.156 2235 Planarity : 0.005 0.104 2607 Dihedral : 4.448 26.140 1992 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.95 % Allowed : 23.46 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.31 (0.19), residues: 1836 helix: 1.16 (0.32), residues: 261 sheet: -0.03 (0.30), residues: 324 loop : -1.66 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 54 TYR 0.013 0.001 TYR J 52 PHE 0.027 0.002 PHE B 108 TRP 0.016 0.001 TRP N 35 HIS 0.007 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00305 (14973) covalent geometry : angle 0.64795 (20325) SS BOND : bond 0.00481 ( 18) SS BOND : angle 2.88084 ( 36) hydrogen bonds : bond 0.04101 ( 457) hydrogen bonds : angle 4.91359 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.515 Fit side-chains REVERT: H 25 SER cc_start: 0.6033 (t) cc_final: 0.5733 (p) REVERT: M 46 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6106 (tp) REVERT: N 4 MET cc_start: 0.6440 (mmt) cc_final: 0.5880 (mmt) REVERT: N 24 ARG cc_start: 0.7055 (ptp90) cc_final: 0.6654 (mtp180) REVERT: N 27 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: N 36 TYR cc_start: 0.6043 (m-80) cc_final: 0.5740 (m-80) REVERT: N 47 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5921 (mp) REVERT: A 150 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7067 (m-40) REVERT: A 174 GLU cc_start: 0.7756 (mp0) cc_final: 0.7003 (mp0) REVERT: A 313 LYS cc_start: 0.8270 (tptt) cc_final: 0.7919 (tptp) REVERT: C 26 VAL cc_start: 0.7887 (t) cc_final: 0.7640 (m) REVERT: E 77 ASP cc_start: 0.7582 (p0) cc_final: 0.7003 (p0) REVERT: E 292 MET cc_start: 0.7211 (mmt) cc_final: 0.6789 (mmt) REVERT: E 313 LYS cc_start: 0.8484 (tptt) cc_final: 0.7928 (tptp) REVERT: B 71 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5666 (mt) REVERT: D 103 GLU cc_start: 0.7190 (tp30) cc_final: 0.6743 (tm-30) REVERT: F 103 GLU cc_start: 0.7312 (tp30) cc_final: 0.6905 (tm-30) outliers start: 64 outliers final: 55 residues processed: 240 average time/residue: 0.1102 time to fit residues: 39.5435 Evaluate side-chains 249 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 108 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 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 = 0.4305 r_free = 0.4305 target = 0.203498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.171874 restraints weight = 20478.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169604 restraints weight = 26049.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.171354 restraints weight = 30159.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172239 restraints weight = 17408.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174235 restraints weight = 15292.058| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14991 Z= 0.136 Angle : 0.669 19.500 20361 Z= 0.331 Chirality : 0.044 0.154 2235 Planarity : 0.005 0.107 2607 Dihedral : 4.504 30.676 1992 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.14 % Allowed : 23.58 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.19), residues: 1836 helix: 1.11 (0.32), residues: 261 sheet: 0.01 (0.30), residues: 324 loop : -1.68 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 54 TYR 0.015 0.001 TYR E 274 PHE 0.026 0.002 PHE B 108 TRP 0.015 0.001 TRP N 35 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00320 (14973) covalent geometry : angle 0.65859 (20325) SS BOND : bond 0.00446 ( 18) SS BOND : angle 2.83975 ( 36) hydrogen bonds : bond 0.04164 ( 457) hydrogen bonds : angle 4.97674 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.530 Fit side-chains REVERT: H 25 SER cc_start: 0.6096 (t) cc_final: 0.5783 (p) REVERT: J 100 TYR cc_start: 0.8524 (m-80) cc_final: 0.8234 (m-80) REVERT: M 46 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6161 (tp) REVERT: N 4 MET cc_start: 0.6425 (mmt) cc_final: 0.5861 (mmt) REVERT: N 24 ARG cc_start: 0.7128 (ptp90) cc_final: 0.6693 (mtp180) REVERT: N 27 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: N 36 TYR cc_start: 0.6135 (m-80) cc_final: 0.5793 (m-80) REVERT: N 47 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6039 (mp) REVERT: N 82 ASP cc_start: 0.7694 (m-30) cc_final: 0.7492 (m-30) REVERT: A 150 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7080 (m-40) REVERT: A 174 GLU cc_start: 0.7676 (mp0) cc_final: 0.6813 (mp0) REVERT: A 278 ASN cc_start: 0.7672 (t0) cc_final: 0.7272 (m110) REVERT: A 313 LYS cc_start: 0.8240 (tptt) cc_final: 0.7932 (tptp) REVERT: C 26 VAL cc_start: 0.7854 (t) cc_final: 0.7561 (m) REVERT: C 268 MET cc_start: 0.7234 (mtp) cc_final: 0.6984 (ttm) REVERT: E 28 THR cc_start: 0.7503 (t) cc_final: 0.7210 (m) REVERT: E 77 ASP cc_start: 0.7615 (p0) cc_final: 0.7093 (p0) REVERT: E 292 MET cc_start: 0.7278 (mmt) cc_final: 0.6853 (mmt) REVERT: E 313 LYS cc_start: 0.8448 (tptt) cc_final: 0.7954 (tptp) REVERT: B 71 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5544 (mp) REVERT: D 103 GLU cc_start: 0.7112 (tp30) cc_final: 0.6677 (tm-30) REVERT: F 103 GLU cc_start: 0.7452 (tp30) cc_final: 0.6890 (tm-30) outliers start: 67 outliers final: 56 residues processed: 241 average time/residue: 0.1186 time to fit residues: 42.3538 Evaluate side-chains 245 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 108 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 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 = 0.4249 r_free = 0.4249 target = 0.197517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165325 restraints weight = 20327.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162962 restraints weight = 26475.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164598 restraints weight = 28075.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165554 restraints weight = 16669.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166165 restraints weight = 14444.348| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14991 Z= 0.210 Angle : 0.756 19.445 20361 Z= 0.381 Chirality : 0.046 0.172 2235 Planarity : 0.005 0.110 2607 Dihedral : 5.036 28.869 1992 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.89 % Allowed : 23.77 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.58 (0.19), residues: 1836 helix: 0.82 (0.32), residues: 261 sheet: -0.17 (0.28), residues: 360 loop : -1.88 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 74 TYR 0.022 0.002 TYR J 52 PHE 0.027 0.002 PHE B 108 TRP 0.022 0.002 TRP N 94 HIS 0.007 0.002 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00506 (14973) covalent geometry : angle 0.74057 (20325) SS BOND : bond 0.00608 ( 18) SS BOND : angle 3.64925 ( 36) hydrogen bonds : bond 0.05012 ( 457) hydrogen bonds : angle 5.35283 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.52 seconds wall clock time: 39 minutes 30.20 seconds (2370.20 seconds total)