Starting phenix.real_space_refine on Mon Apr 6 18:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k22_22640/04_2026/7k22_22640.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k22_22640/04_2026/7k22_22640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k22_22640/04_2026/7k22_22640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k22_22640/04_2026/7k22_22640.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k22_22640/04_2026/7k22_22640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k22_22640/04_2026/7k22_22640.map" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 1.000 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 120 5.16 5 C 13745 2.51 5 N 3610 2.21 5 O 4190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21665 Number of models: 1 Model: "" Number of chains: 3 Chain: "L1" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H1" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "F1" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Restraints were copied for chains: L2, L3, L4, L5, H2, H3, H4, H5, F2, F3, F4, F5 Time building chain proxies: 3.63, per 1000 atoms: 0.17 Number of scatterers: 21665 At special positions: 0 Unit cell: (140.8, 136.4, 124.3, 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 120 16.00 O 4190 8.00 N 3610 7.00 C 13745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYSL1 23 " - pdb=" SG CYSL1 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH1 18 " - pdb=" SG CYSH1 91 " distance=2.03 Simple disulfide: pdb=" SG CYSF1 19 " - pdb=" SG CYSF2 114 " distance=2.03 Simple disulfide: pdb=" SG CYSF1 114 " - pdb=" SG CYSF5 19 " distance=2.03 Simple disulfide: pdb=" SG CYSL2 23 " - pdb=" SG CYSL2 88 " distance=2.03 Simple disulfide: pdb=" SG CYSL3 23 " - pdb=" SG CYSL3 88 " distance=2.03 Simple disulfide: pdb=" SG CYSL4 23 " - pdb=" SG CYSL4 88 " distance=2.03 Simple disulfide: pdb=" SG CYSL5 23 " - pdb=" SG CYSL5 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH2 18 " - pdb=" SG CYSH2 91 " distance=2.03 Simple disulfide: pdb=" SG CYSH3 18 " - pdb=" SG CYSH3 91 " distance=2.03 Simple disulfide: pdb=" SG CYSH4 18 " - pdb=" SG CYSH4 91 " distance=2.03 Simple disulfide: pdb=" SG CYSH5 18 " - pdb=" SG CYSH5 91 " distance=2.03 Simple disulfide: pdb=" SG CYSF2 19 " - pdb=" SG CYSF3 114 " distance=2.06 Simple disulfide: pdb=" SG CYSF3 19 " - pdb=" SG CYSF4 114 " distance=2.07 Simple disulfide: pdb=" SG CYSF4 19 " - pdb=" SG CYSF5 114 " distance=1.93 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: 1.68 Conformation dependent library (CDL) restraints added in 1.0 seconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 45 sheets defined 11.1% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'L1' and resid 50 through 52 No H-bonds generated for 'chain 'L1' and resid 50 through 52' Processing helix chain 'L1' and resid 79 through 83 removed outlier: 3.630A pdb=" N LEUL1 83 " --> pdb=" O THRL1 80 " (cutoff:3.500A) Processing helix chain 'H1' and resid 24 through 28 removed outlier: 3.507A pdb=" N SERH1 27 " --> pdb=" O THRH1 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYRH1 28 " --> pdb=" O PHEH1 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H1' and resid 24 through 28' Processing helix chain 'H1' and resid 57 through 60 removed outlier: 3.982A pdb=" N LYSH1 60 " --> pdb=" O ASPH1 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H1' and resid 57 through 60' Processing helix chain 'F1' and resid 33 through 39 Processing helix chain 'F1' and resid 91 through 95 Processing helix chain 'F1' and resid 132 through 137 Processing helix chain 'F1' and resid 192 through 197 removed outlier: 3.597A pdb=" N ILEF1 196 " --> pdb=" O THRF1 192 " (cutoff:3.500A) Processing helix chain 'F1' and resid 202 through 207 Processing helix chain 'F1' and resid 320 through 322 No H-bonds generated for 'chain 'F1' and resid 320 through 322' Processing helix chain 'F1' and resid 323 through 333 Processing helix chain 'L2' and resid 50 through 52 No H-bonds generated for 'chain 'L2' and resid 50 through 52' Processing helix chain 'L2' and resid 79 through 83 removed outlier: 3.629A pdb=" N LEUL2 83 " --> pdb=" O THRL2 80 " (cutoff:3.500A) Processing helix chain 'H2' and resid 24 through 28 removed outlier: 3.505A pdb=" N SERH2 27 " --> pdb=" O THRH2 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYRH2 28 " --> pdb=" O PHEH2 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 24 through 28' Processing helix chain 'H2' and resid 57 through 60 removed outlier: 3.984A pdb=" N LYSH2 60 " --> pdb=" O ASPH2 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 57 through 60' Processing helix chain 'F2' and resid 33 through 39 Processing helix chain 'F2' and resid 91 through 95 Processing helix chain 'F2' and resid 132 through 137 Processing helix chain 'F2' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF2 196 " --> pdb=" O THRF2 192 " (cutoff:3.500A) Processing helix chain 'F2' and resid 202 through 207 Processing helix chain 'F2' and resid 320 through 322 No H-bonds generated for 'chain 'F2' and resid 320 through 322' Processing helix chain 'F2' and resid 323 through 333 Processing helix chain 'L3' and resid 50 through 52 No H-bonds generated for 'chain 'L3' and resid 50 through 52' Processing helix chain 'L3' and resid 79 through 83 removed outlier: 3.629A pdb=" N LEUL3 83 " --> pdb=" O THRL3 80 " (cutoff:3.500A) Processing helix chain 'H3' and resid 24 through 28 removed outlier: 3.506A pdb=" N SERH3 27 " --> pdb=" O THRH3 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYRH3 28 " --> pdb=" O PHEH3 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H3' and resid 24 through 28' Processing helix chain 'H3' and resid 57 through 60 removed outlier: 3.983A pdb=" N LYSH3 60 " --> pdb=" O ASPH3 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H3' and resid 57 through 60' Processing helix chain 'F3' and resid 33 through 39 Processing helix chain 'F3' and resid 91 through 95 Processing helix chain 'F3' and resid 132 through 137 Processing helix chain 'F3' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF3 196 " --> pdb=" O THRF3 192 " (cutoff:3.500A) Processing helix chain 'F3' and resid 202 through 207 Processing helix chain 'F3' and resid 320 through 322 No H-bonds generated for 'chain 'F3' and resid 320 through 322' Processing helix chain 'F3' and resid 323 through 333 Processing helix chain 'L4' and resid 50 through 52 No H-bonds generated for 'chain 'L4' and resid 50 through 52' Processing helix chain 'L4' and resid 79 through 83 removed outlier: 3.630A pdb=" N LEUL4 83 " --> pdb=" O THRL4 80 " (cutoff:3.500A) Processing helix chain 'H4' and resid 24 through 28 removed outlier: 3.505A pdb=" N SERH4 27 " --> pdb=" O THRH4 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYRH4 28 " --> pdb=" O PHEH4 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H4' and resid 24 through 28' Processing helix chain 'H4' and resid 57 through 60 removed outlier: 3.983A pdb=" N LYSH4 60 " --> pdb=" O ASPH4 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H4' and resid 57 through 60' Processing helix chain 'F4' and resid 33 through 39 Processing helix chain 'F4' and resid 91 through 95 Processing helix chain 'F4' and resid 132 through 137 Processing helix chain 'F4' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF4 196 " --> pdb=" O THRF4 192 " (cutoff:3.500A) Processing helix chain 'F4' and resid 202 through 207 Processing helix chain 'F4' and resid 320 through 322 No H-bonds generated for 'chain 'F4' and resid 320 through 322' Processing helix chain 'F4' and resid 323 through 333 Processing helix chain 'L5' and resid 50 through 52 No H-bonds generated for 'chain 'L5' and resid 50 through 52' Processing helix chain 'L5' and resid 79 through 83 removed outlier: 3.629A pdb=" N LEUL5 83 " --> pdb=" O THRL5 80 " (cutoff:3.500A) Processing helix chain 'H5' and resid 24 through 28 removed outlier: 3.506A pdb=" N SERH5 27 " --> pdb=" O THRH5 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYRH5 28 " --> pdb=" O PHEH5 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H5' and resid 24 through 28' Processing helix chain 'H5' and resid 57 through 60 removed outlier: 3.984A pdb=" N LYSH5 60 " --> pdb=" O ASPH5 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H5' and resid 57 through 60' Processing helix chain 'F5' and resid 33 through 39 Processing helix chain 'F5' and resid 91 through 95 Processing helix chain 'F5' and resid 132 through 137 Processing helix chain 'F5' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF5 196 " --> pdb=" O THRF5 192 " (cutoff:3.500A) Processing helix chain 'F5' and resid 202 through 207 Processing helix chain 'F5' and resid 320 through 322 No H-bonds generated for 'chain 'F5' and resid 320 through 322' Processing helix chain 'F5' and resid 323 through 333 Processing sheet with id=AA1, first strand: chain 'L1' and resid 4 through 6 removed outlier: 6.155A pdb=" N THRL1 69 " --> pdb=" O ALAL1 25 " (cutoff:3.500A) removed outlier: 11.441A pdb=" N GLNL1 27 " --> pdb=" O SERL1 67 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N SERL1 67 " --> pdb=" O GLNL1 27 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N VALL1 29 " --> pdb=" O SERL1 65 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N SERL1 65 " --> pdb=" O VALL1 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L1' and resid 53 through 54 removed outlier: 6.447A pdb=" N TRPL1 35 " --> pdb=" O VALL1 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYRL1 49 " --> pdb=" O VALL1 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL1 33 " --> pdb=" O TYRL1 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H1' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH1 73 " --> pdb=" O ASPH1 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H1' and resid 53 through 55 removed outlier: 5.606A pdb=" N LEUH1 41 " --> pdb=" O VALH1 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH1 36 " --> pdb=" O LEUH1 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH1 43 " --> pdb=" O ARGH1 34 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARGH1 34 " --> pdb=" O TRPH1 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F1' and resid 46 through 53 removed outlier: 6.512A pdb=" N TYRF1 305 " --> pdb=" O THRF1 127 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THRF1 127 " --> pdb=" O TYRF1 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF1 307 " --> pdb=" O VALF1 125 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VALF1 125 " --> pdb=" O LYSF1 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF1 309 " --> pdb=" O VALF1 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F1' and resid 99 through 104 removed outlier: 6.535A pdb=" N ARGF1 300 " --> pdb=" O METF1 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRPF1 288 " --> pdb=" O HISF1 298 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HISF1 298 " --> pdb=" O TRPF1 288 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F1' and resid 99 through 104 Processing sheet with id=AA8, first strand: chain 'F1' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF1 153 " --> pdb=" O PROF1 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F1' and resid 213 through 215 Processing sheet with id=AB1, first strand: chain 'F1' and resid 252 through 256 Processing sheet with id=AB2, first strand: chain 'F1' and resid 252 through 256 removed outlier: 6.534A pdb=" N ARGF2 300 " --> pdb=" O METF2 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRPF2 288 " --> pdb=" O HISF2 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF2 298 " --> pdb=" O TRPF2 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L2' and resid 4 through 6 removed outlier: 6.155A pdb=" N THRL2 69 " --> pdb=" O ALAL2 25 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N GLNL2 27 " --> pdb=" O SERL2 67 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N SERL2 67 " --> pdb=" O GLNL2 27 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N VALL2 29 " --> pdb=" O SERL2 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL2 65 " --> pdb=" O VALL2 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L2' and resid 53 through 54 removed outlier: 6.446A pdb=" N TRPL2 35 " --> pdb=" O VALL2 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYRL2 49 " --> pdb=" O VALL2 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL2 33 " --> pdb=" O TYRL2 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H2' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH2 73 " --> pdb=" O ASPH2 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H2' and resid 53 through 55 removed outlier: 5.606A pdb=" N LEUH2 41 " --> pdb=" O VALH2 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH2 36 " --> pdb=" O LEUH2 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH2 43 " --> pdb=" O ARGH2 34 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARGH2 34 " --> pdb=" O TRPH2 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F2' and resid 46 through 53 removed outlier: 6.513A pdb=" N TYRF2 305 " --> pdb=" O THRF2 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF2 127 " --> pdb=" O TYRF2 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF2 307 " --> pdb=" O VALF2 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF2 125 " --> pdb=" O LYSF2 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF2 309 " --> pdb=" O VALF2 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F2' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF2 153 " --> pdb=" O PROF2 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F2' and resid 213 through 215 Processing sheet with id=AC1, first strand: chain 'F2' and resid 252 through 256 Processing sheet with id=AC2, first strand: chain 'F2' and resid 252 through 256 removed outlier: 6.534A pdb=" N ARGF3 300 " --> pdb=" O METF3 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRPF3 288 " --> pdb=" O HISF3 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF3 298 " --> pdb=" O TRPF3 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L3' and resid 4 through 6 removed outlier: 6.156A pdb=" N THRL3 69 " --> pdb=" O ALAL3 25 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N GLNL3 27 " --> pdb=" O SERL3 67 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N SERL3 67 " --> pdb=" O GLNL3 27 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N VALL3 29 " --> pdb=" O SERL3 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL3 65 " --> pdb=" O VALL3 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L3' and resid 53 through 54 removed outlier: 6.447A pdb=" N TRPL3 35 " --> pdb=" O VALL3 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYRL3 49 " --> pdb=" O VALL3 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL3 33 " --> pdb=" O TYRL3 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H3' and resid 18 through 19 removed outlier: 3.803A pdb=" N THRH3 73 " --> pdb=" O ASPH3 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H3' and resid 53 through 55 removed outlier: 5.605A pdb=" N LEUH3 41 " --> pdb=" O VALH3 36 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VALH3 36 " --> pdb=" O LEUH3 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH3 43 " --> pdb=" O ARGH3 34 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARGH3 34 " --> pdb=" O TRPH3 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F3' and resid 46 through 53 removed outlier: 6.513A pdb=" N TYRF3 305 " --> pdb=" O THRF3 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF3 127 " --> pdb=" O TYRF3 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF3 307 " --> pdb=" O VALF3 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF3 125 " --> pdb=" O LYSF3 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF3 309 " --> pdb=" O VALF3 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F3' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF3 153 " --> pdb=" O PROF3 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F3' and resid 213 through 215 Processing sheet with id=AD1, first strand: chain 'F3' and resid 252 through 256 Processing sheet with id=AD2, first strand: chain 'F3' and resid 252 through 256 removed outlier: 6.535A pdb=" N ARGF4 300 " --> pdb=" O METF4 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRPF4 288 " --> pdb=" O HISF4 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF4 298 " --> pdb=" O TRPF4 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L4' and resid 4 through 6 removed outlier: 6.156A pdb=" N THRL4 69 " --> pdb=" O ALAL4 25 " (cutoff:3.500A) removed outlier: 11.441A pdb=" N GLNL4 27 " --> pdb=" O SERL4 67 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N SERL4 67 " --> pdb=" O GLNL4 27 " (cutoff:3.500A) removed outlier: 12.020A pdb=" N VALL4 29 " --> pdb=" O SERL4 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL4 65 " --> pdb=" O VALL4 29 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L4' and resid 53 through 54 removed outlier: 6.446A pdb=" N TRPL4 35 " --> pdb=" O VALL4 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYRL4 49 " --> pdb=" O VALL4 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL4 33 " --> pdb=" O TYRL4 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H4' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH4 73 " --> pdb=" O ASPH4 68 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H4' and resid 53 through 55 removed outlier: 5.605A pdb=" N LEUH4 41 " --> pdb=" O VALH4 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH4 36 " --> pdb=" O LEUH4 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH4 43 " --> pdb=" O ARGH4 34 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARGH4 34 " --> pdb=" O TRPH4 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F4' and resid 46 through 53 removed outlier: 6.512A pdb=" N TYRF4 305 " --> pdb=" O THRF4 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF4 127 " --> pdb=" O TYRF4 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF4 307 " --> pdb=" O VALF4 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF4 125 " --> pdb=" O LYSF4 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF4 309 " --> pdb=" O VALF4 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F4' and resid 144 through 146 removed outlier: 6.188A pdb=" N ILEF4 153 " --> pdb=" O PROF4 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F4' and resid 213 through 215 Processing sheet with id=AE1, first strand: chain 'F4' and resid 252 through 256 Processing sheet with id=AE2, first strand: chain 'F4' and resid 252 through 256 removed outlier: 6.535A pdb=" N ARGF5 300 " --> pdb=" O METF5 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRPF5 288 " --> pdb=" O HISF5 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF5 298 " --> pdb=" O TRPF5 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L5' and resid 4 through 6 removed outlier: 6.156A pdb=" N THRL5 69 " --> pdb=" O ALAL5 25 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N GLNL5 27 " --> pdb=" O SERL5 67 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N SERL5 67 " --> pdb=" O GLNL5 27 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N VALL5 29 " --> pdb=" O SERL5 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL5 65 " --> pdb=" O VALL5 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L5' and resid 53 through 54 removed outlier: 6.447A pdb=" N TRPL5 35 " --> pdb=" O VALL5 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYRL5 49 " --> pdb=" O VALL5 33 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VALL5 33 " --> pdb=" O TYRL5 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H5' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH5 73 " --> pdb=" O ASPH5 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H5' and resid 53 through 55 removed outlier: 5.606A pdb=" N LEUH5 41 " --> pdb=" O VALH5 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH5 36 " --> pdb=" O LEUH5 41 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRPH5 43 " --> pdb=" O ARGH5 34 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARGH5 34 " --> pdb=" O TRPH5 43 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F5' and resid 46 through 53 removed outlier: 6.513A pdb=" N TYRF5 305 " --> pdb=" O THRF5 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF5 127 " --> pdb=" O TYRF5 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF5 307 " --> pdb=" O VALF5 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF5 125 " --> pdb=" O LYSF5 307 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THRF5 309 " --> pdb=" O VALF5 123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F5' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF5 153 " --> pdb=" O PROF5 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F5' and resid 213 through 215 646 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.30 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: 6960 1.34 - 1.46: 4681 1.46 - 1.57: 10384 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 22225 Sorted by residual: bond pdb=" CA GLNF2 71 " pdb=" C GLNF2 71 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.48e+00 bond pdb=" CA GLNF3 71 " pdb=" C GLNF3 71 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.44e+00 bond pdb=" CA GLNF1 71 " pdb=" C GLNF1 71 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.42e+00 bond pdb=" CA GLNF5 71 " pdb=" C GLNF5 71 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.26e+00 bond pdb=" CA GLNF4 71 " pdb=" C GLNF4 71 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.13e+00 ... (remaining 22220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 29430 2.04 - 4.08: 767 4.08 - 6.12: 78 6.12 - 8.16: 10 8.16 - 10.20: 5 Bond angle restraints: 30290 Sorted by residual: angle pdb=" C ALAF3 18 " pdb=" N CYSF3 19 " pdb=" CA CYSF3 19 " ideal model delta sigma weight residual 121.48 111.28 10.20 2.04e+00 2.40e-01 2.50e+01 angle pdb=" C ALAF5 18 " pdb=" N CYSF5 19 " pdb=" CA CYSF5 19 " ideal model delta sigma weight residual 121.48 111.28 10.20 2.04e+00 2.40e-01 2.50e+01 angle pdb=" C ALAF2 18 " pdb=" N CYSF2 19 " pdb=" CA CYSF2 19 " ideal model delta sigma weight residual 121.48 111.29 10.19 2.04e+00 2.40e-01 2.50e+01 angle pdb=" C ALAF4 18 " pdb=" N CYSF4 19 " pdb=" CA CYSF4 19 " ideal model delta sigma weight residual 121.48 111.30 10.18 2.04e+00 2.40e-01 2.49e+01 angle pdb=" C ALAF1 18 " pdb=" N CYSF1 19 " pdb=" CA CYSF1 19 " ideal model delta sigma weight residual 121.48 111.32 10.16 2.04e+00 2.40e-01 2.48e+01 ... (remaining 30285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 11379 17.30 - 34.60: 1367 34.60 - 51.89: 334 51.89 - 69.19: 135 69.19 - 86.49: 30 Dihedral angle restraints: 13245 sinusoidal: 5295 harmonic: 7950 Sorted by residual: dihedral pdb=" CB CYSF3 19 " pdb=" SG CYSF3 19 " pdb=" SG CYSF4 114 " pdb=" CB CYSF4 114 " ideal model delta sinusoidal sigma weight residual -86.00 -150.84 64.84 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYSF1 19 " pdb=" SG CYSF1 19 " pdb=" SG CYSF2 114 " pdb=" CB CYSF2 114 " ideal model delta sinusoidal sigma weight residual -86.00 -150.70 64.70 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYSF4 19 " pdb=" SG CYSF4 19 " pdb=" SG CYSF5 114 " pdb=" CB CYSF5 114 " ideal model delta sinusoidal sigma weight residual -86.00 -150.44 64.44 1 1.00e+01 1.00e-02 5.46e+01 ... (remaining 13242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1941 0.036 - 0.072: 1007 0.072 - 0.108: 282 0.108 - 0.144: 88 0.144 - 0.181: 17 Chirality restraints: 3335 Sorted by residual: chirality pdb=" CA THRF3 62 " pdb=" N THRF3 62 " pdb=" C THRF3 62 " pdb=" CB THRF3 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA THRF1 62 " pdb=" N THRF1 62 " pdb=" C THRF1 62 " pdb=" CB THRF1 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA THRF4 62 " pdb=" N THRF4 62 " pdb=" C THRF4 62 " pdb=" CB THRF4 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 3332 not shown) Planarity restraints: 3905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SERF4 89 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PROF4 90 " 0.109 5.00e-02 4.00e+02 pdb=" CA PROF4 90 " -0.033 5.00e-02 4.00e+02 pdb=" CD PROF4 90 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF3 89 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.38e+00 pdb=" N PROF3 90 " -0.109 5.00e-02 4.00e+02 pdb=" CA PROF3 90 " 0.033 5.00e-02 4.00e+02 pdb=" CD PROF3 90 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF2 89 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PROF2 90 " -0.109 5.00e-02 4.00e+02 pdb=" CA PROF2 90 " 0.033 5.00e-02 4.00e+02 pdb=" CD PROF2 90 " 0.035 5.00e-02 4.00e+02 ... (remaining 3902 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 424 2.65 - 3.21: 19012 3.21 - 3.77: 31867 3.77 - 4.34: 46117 4.34 - 4.90: 76935 Nonbonded interactions: 174355 Sorted by model distance: nonbonded pdb=" OG SERH5 48 " pdb=" OD1 ASPH5 52 " model vdw 2.087 3.040 nonbonded pdb=" OG SERH2 48 " pdb=" OD1 ASPH2 52 " model vdw 2.087 3.040 nonbonded pdb=" OG SERH1 48 " pdb=" OD1 ASPH1 52 " model vdw 2.087 3.040 nonbonded pdb=" OG SERH4 48 " pdb=" OD1 ASPH4 52 " model vdw 2.087 3.040 nonbonded pdb=" OG SERH3 48 " pdb=" OD1 ASPH3 52 " model vdw 2.088 3.040 ... (remaining 174350 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: 0.06 Found NCS groups: ncs_group { reference = chain 'L1' selection = chain 'L2' selection = chain 'L3' selection = chain 'L4' selection = chain 'L5' } ncs_group { reference = chain 'H1' selection = chain 'H2' selection = chain 'H3' selection = chain 'H4' selection = chain 'H5' } ncs_group { reference = chain 'F1' selection = chain 'F2' selection = chain 'F3' selection = chain 'F4' selection = chain 'F5' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.007 0.104 22240 Z= 0.290 Angle : 0.767 10.199 30320 Z= 0.420 Chirality : 0.047 0.181 3335 Planarity : 0.005 0.063 3905 Dihedral : 17.163 86.487 8130 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.96 % Favored : 88.86 % Rotamer: Outliers : 8.26 % Allowed : 16.32 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -4.13 (0.13), residues: 2720 helix: -4.13 (0.17), residues: 125 sheet: -1.40 (0.18), residues: 755 loop : -3.49 (0.11), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGF5 56 TYR 0.013 0.002 TYRF1 239 PHE 0.021 0.002 PHEF2 165 TRP 0.016 0.002 TRPH1 104 HIS 0.005 0.002 HISF5 139 Details of bonding type rmsd covalent geometry : bond 0.00680 (22225) covalent geometry : angle 0.76493 (30290) SS BOND : bond 0.02967 ( 15) SS BOND : angle 2.10803 ( 30) hydrogen bonds : bond 0.18732 ( 560) hydrogen bonds : angle 8.54360 ( 1503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 312 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: L1 78 ILE cc_start: 0.8098 (mm) cc_final: 0.7673 (mm) REVERT: L1 79 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7070 (mm-40) REVERT: H1 99 ASP cc_start: 0.8649 (m-30) cc_final: 0.8386 (m-30) REVERT: F1 56 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7629 (mtt-85) REVERT: F1 103 LEU cc_start: 0.8532 (mt) cc_final: 0.8221 (mp) REVERT: F1 111 ASP cc_start: 0.7599 (t0) cc_final: 0.7275 (t0) REVERT: F1 274 LYS cc_start: 0.8013 (mttt) cc_final: 0.7774 (mtpt) REVERT: F1 313 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.8410 (ttm-80) REVERT: L2 79 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7209 (tp40) REVERT: H2 57 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5871 (m-30) REVERT: F2 111 ASP cc_start: 0.7577 (t0) cc_final: 0.6916 (t0) REVERT: H3 36 VAL cc_start: 0.6119 (OUTLIER) cc_final: 0.5908 (p) REVERT: H3 67 ARG cc_start: 0.9011 (ptm160) cc_final: 0.8807 (ptp-170) REVERT: F3 100 MET cc_start: 0.8574 (ppp) cc_final: 0.8310 (ppp) REVERT: F3 111 ASP cc_start: 0.7011 (t0) cc_final: 0.6457 (t0) REVERT: F3 143 LYS cc_start: 0.8417 (tttt) cc_final: 0.8184 (ttpp) REVERT: F3 208 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8345 (tt) REVERT: F3 221 MET cc_start: 0.7601 (mmm) cc_final: 0.7293 (mmm) REVERT: L4 78 ILE cc_start: 0.7916 (mm) cc_final: 0.7700 (mm) REVERT: L4 79 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7235 (mm-40) REVERT: L4 95 PRO cc_start: 0.8470 (Cg_endo) cc_final: 0.8182 (Cg_exo) REVERT: F4 56 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7576 (mtt-85) REVERT: F4 111 ASP cc_start: 0.7755 (t0) cc_final: 0.7104 (t0) REVERT: L5 27 GLN cc_start: 0.7097 (mt0) cc_final: 0.6870 (mt0) REVERT: L5 78 ILE cc_start: 0.7841 (mm) cc_final: 0.7522 (mm) REVERT: L5 95 PRO cc_start: 0.8353 (Cg_endo) cc_final: 0.8037 (Cg_exo) REVERT: F5 56 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7767 (mtt-85) REVERT: F5 103 LEU cc_start: 0.8585 (mt) cc_final: 0.8240 (mp) REVERT: F5 111 ASP cc_start: 0.7484 (t0) cc_final: 0.7016 (t0) REVERT: F5 208 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8502 (tt) REVERT: F5 286 MET cc_start: 0.8491 (mmm) cc_final: 0.8258 (mmm) outliers start: 200 outliers final: 110 residues processed: 490 average time/residue: 0.1562 time to fit residues: 117.8871 Evaluate side-chains 397 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 277 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 21 MET Chi-restraints excluded: chain L1 residue 33 VAL Chi-restraints excluded: chain L1 residue 56 THR Chi-restraints excluded: chain L1 residue 72 THR Chi-restraints excluded: chain L1 residue 74 THR Chi-restraints excluded: chain L1 residue 79 GLN Chi-restraints excluded: chain L1 residue 85 VAL Chi-restraints excluded: chain H1 residue 24 THR Chi-restraints excluded: chain H1 residue 49 SER Chi-restraints excluded: chain H1 residue 51 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain F1 residue 19 CYS Chi-restraints excluded: chain F1 residue 56 ARG Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 123 VAL Chi-restraints excluded: chain F1 residue 153 ILE Chi-restraints excluded: chain F1 residue 177 LEU Chi-restraints excluded: chain F1 residue 178 VAL Chi-restraints excluded: chain F1 residue 217 ASP Chi-restraints excluded: chain F1 residue 310 LEU Chi-restraints excluded: chain F1 residue 344 GLU Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain L2 residue 21 MET Chi-restraints excluded: chain L2 residue 72 THR Chi-restraints excluded: chain L2 residue 74 THR Chi-restraints excluded: chain L2 residue 79 GLN Chi-restraints excluded: chain H2 residue 49 SER Chi-restraints excluded: chain H2 residue 51 SER Chi-restraints excluded: chain H2 residue 57 ASP Chi-restraints excluded: chain H2 residue 112 THR Chi-restraints excluded: chain F2 residue 19 CYS Chi-restraints excluded: chain F2 residue 56 ARG Chi-restraints excluded: chain F2 residue 76 SER Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 88 ASP Chi-restraints excluded: chain F2 residue 123 VAL Chi-restraints excluded: chain F2 residue 153 ILE Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 178 VAL Chi-restraints excluded: chain F2 residue 217 ASP Chi-restraints excluded: chain F2 residue 310 LEU Chi-restraints excluded: chain F2 residue 344 GLU Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 369 TYR Chi-restraints excluded: chain L3 residue 21 MET Chi-restraints excluded: chain L3 residue 33 VAL Chi-restraints excluded: chain L3 residue 72 THR Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain H3 residue 49 SER Chi-restraints excluded: chain H3 residue 51 SER Chi-restraints excluded: chain H3 residue 57 ASP Chi-restraints excluded: chain H3 residue 112 THR Chi-restraints excluded: chain F3 residue 19 CYS Chi-restraints excluded: chain F3 residue 56 ARG Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 76 SER Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 153 ILE Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 217 ASP Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 310 LEU Chi-restraints excluded: chain F3 residue 344 GLU Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 369 TYR Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain L4 residue 33 VAL Chi-restraints excluded: chain L4 residue 72 THR Chi-restraints excluded: chain L4 residue 74 THR Chi-restraints excluded: chain L4 residue 79 GLN Chi-restraints excluded: chain L4 residue 85 VAL Chi-restraints excluded: chain H4 residue 49 SER Chi-restraints excluded: chain H4 residue 51 SER Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain H4 residue 112 THR Chi-restraints excluded: chain F4 residue 19 CYS Chi-restraints excluded: chain F4 residue 56 ARG Chi-restraints excluded: chain F4 residue 76 SER Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 123 VAL Chi-restraints excluded: chain F4 residue 153 ILE Chi-restraints excluded: chain F4 residue 177 LEU Chi-restraints excluded: chain F4 residue 178 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 217 ASP Chi-restraints excluded: chain F4 residue 282 CYS Chi-restraints excluded: chain F4 residue 310 LEU Chi-restraints excluded: chain F4 residue 344 GLU Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 368 ARG Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 33 VAL Chi-restraints excluded: chain L5 residue 72 THR Chi-restraints excluded: chain L5 residue 74 THR Chi-restraints excluded: chain L5 residue 85 VAL Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 49 SER Chi-restraints excluded: chain H5 residue 51 SER Chi-restraints excluded: chain H5 residue 112 THR Chi-restraints excluded: chain F5 residue 19 CYS Chi-restraints excluded: chain F5 residue 56 ARG Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 76 SER Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 88 ASP Chi-restraints excluded: chain F5 residue 153 ILE Chi-restraints excluded: chain F5 residue 177 LEU Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 217 ASP Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 344 GLU Chi-restraints excluded: chain F5 residue 365 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1 6 GLN H1 69 ASN F1 54 ASN ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 80 ASN F1 142 ASN F1 228 HIS F1 254 GLN F1 293 ASN F1 339 GLN F1 347 GLN L2 6 GLN H2 69 ASN F2 54 ASN F2 80 ASN F2 142 ASN ** F2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2 254 GLN F2 293 ASN F2 339 GLN F2 347 GLN L3 6 GLN H3 69 ASN F3 54 ASN ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 80 ASN F3 142 ASN F3 254 GLN F3 293 ASN F3 339 GLN F3 347 GLN L4 6 GLN H4 69 ASN F4 54 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 80 ASN F4 142 ASN ** F4 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F4 254 GLN F4 293 ASN F4 339 GLN F4 347 GLN L5 6 GLN H5 69 ASN F5 54 ASN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 80 ASN F5 142 ASN F5 163 HIS ** F5 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F5 254 GLN F5 293 ASN F5 339 GLN F5 347 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.162911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.130232 restraints weight = 22653.358| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.13 r_work: 0.3043 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22240 Z= 0.117 Angle : 0.612 7.658 30320 Z= 0.315 Chirality : 0.044 0.156 3335 Planarity : 0.004 0.049 3905 Dihedral : 9.596 84.911 3198 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.45 % Allowed : 18.18 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -3.20 (0.15), residues: 2720 helix: -3.15 (0.39), residues: 120 sheet: -0.97 (0.18), residues: 765 loop : -2.76 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGF3 313 TYR 0.014 0.001 TYRL3 49 PHE 0.014 0.001 PHEF3 165 TRP 0.016 0.001 TRPH2 104 HIS 0.005 0.002 HISF4 139 Details of bonding type rmsd covalent geometry : bond 0.00274 (22225) covalent geometry : angle 0.61224 (30290) SS BOND : bond 0.00340 ( 15) SS BOND : angle 0.82458 ( 30) hydrogen bonds : bond 0.03029 ( 560) hydrogen bonds : angle 5.80802 ( 1503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 311 time to evaluate : 0.762 Fit side-chains REVERT: L1 78 ILE cc_start: 0.7579 (mm) cc_final: 0.7130 (mm) REVERT: H1 99 ASP cc_start: 0.8723 (m-30) cc_final: 0.8450 (m-30) REVERT: F1 103 LEU cc_start: 0.8396 (mt) cc_final: 0.8014 (mp) REVERT: F1 111 ASP cc_start: 0.7330 (t0) cc_final: 0.6805 (t0) REVERT: F1 284 ASP cc_start: 0.8542 (m-30) cc_final: 0.8340 (m-30) REVERT: H2 30 MET cc_start: 0.8236 (mmm) cc_final: 0.7898 (mmm) REVERT: H2 57 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.6079 (m-30) REVERT: F2 103 LEU cc_start: 0.8583 (mt) cc_final: 0.8293 (mp) REVERT: F2 111 ASP cc_start: 0.7597 (t0) cc_final: 0.6820 (t0) REVERT: F2 235 GLU cc_start: 0.7094 (mp0) cc_final: 0.6863 (mp0) REVERT: F2 342 GLU cc_start: 0.7434 (mp0) cc_final: 0.6991 (mp0) REVERT: H3 36 VAL cc_start: 0.5862 (OUTLIER) cc_final: 0.5608 (p) REVERT: F3 111 ASP cc_start: 0.7122 (t0) cc_final: 0.6451 (t0) REVERT: F3 143 LYS cc_start: 0.8625 (tttt) cc_final: 0.8352 (ttpp) REVERT: F3 208 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8562 (tt) REVERT: L4 12 SER cc_start: 0.7097 (OUTLIER) cc_final: 0.6673 (p) REVERT: L4 95 PRO cc_start: 0.8354 (Cg_endo) cc_final: 0.8088 (Cg_exo) REVERT: F4 111 ASP cc_start: 0.7602 (t0) cc_final: 0.6889 (t0) REVERT: F4 235 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6502 (mm-30) REVERT: F4 274 LYS cc_start: 0.8319 (mttp) cc_final: 0.8072 (mtpp) REVERT: L5 78 ILE cc_start: 0.7388 (mm) cc_final: 0.7099 (mm) REVERT: F5 103 LEU cc_start: 0.8441 (mt) cc_final: 0.8081 (mp) REVERT: F5 111 ASP cc_start: 0.7496 (t0) cc_final: 0.6996 (t0) REVERT: F5 242 ASN cc_start: 0.8670 (p0) cc_final: 0.8435 (p0) REVERT: F5 358 GLU cc_start: 0.5608 (mp0) cc_final: 0.4494 (pt0) outliers start: 132 outliers final: 85 residues processed: 418 average time/residue: 0.1336 time to fit residues: 91.4537 Evaluate side-chains 368 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 279 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 74 THR Chi-restraints excluded: chain L1 residue 89 LEU Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 51 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain F1 residue 40 VAL Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 177 LEU Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 297 HIS Chi-restraints excluded: chain F1 residue 310 LEU Chi-restraints excluded: chain F1 residue 344 GLU Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain F1 residue 369 TYR Chi-restraints excluded: chain L2 residue 74 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain H2 residue 51 SER Chi-restraints excluded: chain H2 residue 57 ASP Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 297 HIS Chi-restraints excluded: chain F2 residue 310 LEU Chi-restraints excluded: chain F2 residue 344 GLU Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain H3 residue 51 SER Chi-restraints excluded: chain H3 residue 57 ASP Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 153 ILE Chi-restraints excluded: chain F3 residue 190 VAL Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 310 LEU Chi-restraints excluded: chain F3 residue 344 GLU Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain L4 residue 12 SER Chi-restraints excluded: chain L4 residue 74 THR Chi-restraints excluded: chain L4 residue 89 LEU Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain H4 residue 51 SER Chi-restraints excluded: chain H4 residue 112 THR Chi-restraints excluded: chain F4 residue 19 CYS Chi-restraints excluded: chain F4 residue 40 VAL Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 132 SER Chi-restraints excluded: chain F4 residue 153 ILE Chi-restraints excluded: chain F4 residue 177 LEU Chi-restraints excluded: chain F4 residue 187 GLU Chi-restraints excluded: chain F4 residue 190 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 297 HIS Chi-restraints excluded: chain F4 residue 310 LEU Chi-restraints excluded: chain F4 residue 321 MET Chi-restraints excluded: chain F4 residue 344 GLU Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain L5 residue 74 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain H5 residue 51 SER Chi-restraints excluded: chain H5 residue 112 THR Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 153 ILE Chi-restraints excluded: chain F5 residue 177 LEU Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 297 HIS Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 344 GLU Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 163 HIS ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.158099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.114154 restraints weight = 22847.891| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.37 r_work: 0.2920 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22240 Z= 0.212 Angle : 0.677 9.834 30320 Z= 0.341 Chirality : 0.046 0.162 3335 Planarity : 0.005 0.047 3905 Dihedral : 8.520 75.271 3084 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 6.12 % Allowed : 18.47 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.90 (0.15), residues: 2720 helix: -2.87 (0.39), residues: 120 sheet: -0.90 (0.18), residues: 795 loop : -2.50 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGF1 292 TYR 0.020 0.001 TYRH3 46 PHE 0.018 0.002 PHEF4 165 TRP 0.014 0.002 TRPH3 104 HIS 0.005 0.002 HISF4 297 Details of bonding type rmsd covalent geometry : bond 0.00527 (22225) covalent geometry : angle 0.67646 (30290) SS BOND : bond 0.00231 ( 15) SS BOND : angle 0.84192 ( 30) hydrogen bonds : bond 0.03305 ( 560) hydrogen bonds : angle 5.63310 ( 1503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 268 time to evaluate : 0.835 Fit side-chains REVERT: F1 103 LEU cc_start: 0.8422 (mt) cc_final: 0.8062 (mp) REVERT: F1 111 ASP cc_start: 0.7630 (t0) cc_final: 0.7034 (t0) REVERT: F1 114 CYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6939 (p) REVERT: F1 345 ASN cc_start: 0.8395 (m-40) cc_final: 0.8180 (m110) REVERT: H2 30 MET cc_start: 0.8364 (mmm) cc_final: 0.8010 (mmm) REVERT: H2 57 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.6052 (m-30) REVERT: F2 103 LEU cc_start: 0.8653 (mt) cc_final: 0.8391 (mp) REVERT: F2 111 ASP cc_start: 0.7467 (t0) cc_final: 0.6750 (t0) REVERT: F2 235 GLU cc_start: 0.7274 (mp0) cc_final: 0.7053 (mp0) REVERT: F2 308 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8917 (mt) REVERT: F2 342 GLU cc_start: 0.7747 (mp0) cc_final: 0.7537 (mt-10) REVERT: L3 95 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7901 (Cg_exo) REVERT: H3 36 VAL cc_start: 0.6146 (OUTLIER) cc_final: 0.5894 (p) REVERT: F3 111 ASP cc_start: 0.7636 (t0) cc_final: 0.6828 (t0) REVERT: F3 143 LYS cc_start: 0.8814 (tttt) cc_final: 0.8530 (ttpp) REVERT: F3 208 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8483 (tt) REVERT: F3 225 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8520 (pt0) REVERT: F3 260 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8886 (t) REVERT: F3 286 MET cc_start: 0.8949 (mmm) cc_final: 0.8706 (mmm) REVERT: L4 12 SER cc_start: 0.6448 (OUTLIER) cc_final: 0.6150 (p) REVERT: L4 95 PRO cc_start: 0.8412 (Cg_endo) cc_final: 0.8201 (Cg_exo) REVERT: F4 103 LEU cc_start: 0.8708 (mt) cc_final: 0.8362 (mp) REVERT: F4 111 ASP cc_start: 0.7667 (t0) cc_final: 0.6936 (t0) REVERT: F4 274 LYS cc_start: 0.8405 (mttp) cc_final: 0.8123 (mtpp) REVERT: F5 103 LEU cc_start: 0.8512 (mt) cc_final: 0.8164 (mp) REVERT: F5 111 ASP cc_start: 0.7377 (t0) cc_final: 0.6794 (t0) REVERT: F5 119 MET cc_start: 0.9156 (ptm) cc_final: 0.8942 (ptm) REVERT: F5 208 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8733 (tt) outliers start: 148 outliers final: 103 residues processed: 389 average time/residue: 0.1327 time to fit residues: 84.8275 Evaluate side-chains 378 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 266 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 69 THR Chi-restraints excluded: chain L1 residue 74 THR Chi-restraints excluded: chain L1 residue 89 LEU Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 57 ASP Chi-restraints excluded: chain F1 residue 40 VAL Chi-restraints excluded: chain F1 residue 76 SER Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 114 CYS Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 177 LEU Chi-restraints excluded: chain F1 residue 178 VAL Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 225 GLU Chi-restraints excluded: chain F1 residue 260 THR Chi-restraints excluded: chain F1 residue 297 HIS Chi-restraints excluded: chain F1 residue 308 ILE Chi-restraints excluded: chain F1 residue 310 LEU Chi-restraints excluded: chain F1 residue 344 GLU Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain F1 residue 369 TYR Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 74 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain H2 residue 57 ASP Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 66 LEU Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 225 GLU Chi-restraints excluded: chain F2 residue 260 THR Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 297 HIS Chi-restraints excluded: chain F2 residue 308 ILE Chi-restraints excluded: chain F2 residue 310 LEU Chi-restraints excluded: chain F2 residue 344 GLU Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain F2 residue 369 TYR Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 72 THR Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain H3 residue 57 ASP Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 153 ILE Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 225 GLU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 260 THR Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 310 LEU Chi-restraints excluded: chain F3 residue 344 GLU Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain L4 residue 12 SER Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain L4 residue 74 THR Chi-restraints excluded: chain L4 residue 89 LEU Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain F4 residue 40 VAL Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 132 SER Chi-restraints excluded: chain F4 residue 148 VAL Chi-restraints excluded: chain F4 residue 153 ILE Chi-restraints excluded: chain F4 residue 177 LEU Chi-restraints excluded: chain F4 residue 178 VAL Chi-restraints excluded: chain F4 residue 187 GLU Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 297 HIS Chi-restraints excluded: chain F4 residue 310 LEU Chi-restraints excluded: chain F4 residue 344 GLU Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 369 TYR Chi-restraints excluded: chain L5 residue 12 SER Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 74 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 19 CYS Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 100 MET Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 153 ILE Chi-restraints excluded: chain F5 residue 177 LEU Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 207 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 297 HIS Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 344 GLU Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 135 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 228 HIS F2 345 ASN ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3157 r_free = 0.3157 target = 0.115094 restraints weight = 22691.865| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.36 r_work: 0.2961 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22240 Z= 0.153 Angle : 0.614 9.189 30320 Z= 0.311 Chirality : 0.044 0.146 3335 Planarity : 0.004 0.041 3905 Dihedral : 7.652 78.015 3068 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.62 % Allowed : 19.55 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.62 (0.15), residues: 2720 helix: -2.56 (0.42), residues: 120 sheet: -0.68 (0.18), residues: 795 loop : -2.32 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGF3 313 TYR 0.016 0.001 TYRH3 46 PHE 0.015 0.001 PHEF4 165 TRP 0.014 0.001 TRPH4 104 HIS 0.005 0.002 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00377 (22225) covalent geometry : angle 0.61394 (30290) SS BOND : bond 0.00148 ( 15) SS BOND : angle 0.78002 ( 30) hydrogen bonds : bond 0.02940 ( 560) hydrogen bonds : angle 5.32465 ( 1503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 273 time to evaluate : 0.829 Fit side-chains REVERT: H1 103 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7242 (t70) REVERT: F1 103 LEU cc_start: 0.8361 (mt) cc_final: 0.8001 (mp) REVERT: F1 111 ASP cc_start: 0.7581 (t0) cc_final: 0.6970 (t0) REVERT: F1 219 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8068 (t0) REVERT: H2 30 MET cc_start: 0.8316 (mmm) cc_final: 0.7987 (mmm) REVERT: H2 57 ASP cc_start: 0.6224 (OUTLIER) cc_final: 0.5946 (m-30) REVERT: F2 103 LEU cc_start: 0.8619 (mt) cc_final: 0.8367 (mp) REVERT: F2 111 ASP cc_start: 0.7393 (t0) cc_final: 0.6793 (t0) REVERT: F2 235 GLU cc_start: 0.7255 (mp0) cc_final: 0.7042 (mp0) REVERT: F2 308 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8883 (mt) REVERT: F2 342 GLU cc_start: 0.7782 (mp0) cc_final: 0.7040 (mp0) REVERT: H3 36 VAL cc_start: 0.5946 (OUTLIER) cc_final: 0.5715 (p) REVERT: F3 111 ASP cc_start: 0.7325 (t0) cc_final: 0.6636 (t0) REVERT: F3 143 LYS cc_start: 0.8797 (tttt) cc_final: 0.8514 (ttpp) REVERT: F3 208 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8527 (tt) REVERT: F3 219 ASP cc_start: 0.8002 (t0) cc_final: 0.7783 (t70) REVERT: F3 260 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8893 (t) REVERT: F3 342 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F4 34 MET cc_start: 0.8939 (mmt) cc_final: 0.8682 (mmt) REVERT: F4 111 ASP cc_start: 0.7564 (t0) cc_final: 0.6845 (t0) REVERT: F4 274 LYS cc_start: 0.8359 (mttp) cc_final: 0.8158 (mtpp) REVERT: F4 311 ARG cc_start: 0.8421 (ptt180) cc_final: 0.8138 (ptt180) REVERT: L5 95 PRO cc_start: 0.8370 (Cg_endo) cc_final: 0.8117 (Cg_exo) REVERT: F5 103 LEU cc_start: 0.8450 (mt) cc_final: 0.8088 (mp) REVERT: F5 111 ASP cc_start: 0.7304 (t0) cc_final: 0.6754 (t0) REVERT: F5 208 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8704 (tt) REVERT: F5 219 ASP cc_start: 0.7983 (t0) cc_final: 0.7721 (t70) REVERT: F5 242 ASN cc_start: 0.8568 (p0) cc_final: 0.8328 (p0) REVERT: F5 260 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8896 (t) outliers start: 136 outliers final: 92 residues processed: 382 average time/residue: 0.1327 time to fit residues: 83.2042 Evaluate side-chains 367 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 265 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 69 THR Chi-restraints excluded: chain L1 residue 74 THR Chi-restraints excluded: chain L1 residue 89 LEU Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 57 ASP Chi-restraints excluded: chain H1 residue 103 ASP Chi-restraints excluded: chain F1 residue 76 SER Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 177 LEU Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 219 ASP Chi-restraints excluded: chain F1 residue 260 THR Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 297 HIS Chi-restraints excluded: chain F1 residue 344 GLU Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain F1 residue 369 TYR Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 74 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain H2 residue 57 ASP Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 297 HIS Chi-restraints excluded: chain F2 residue 308 ILE Chi-restraints excluded: chain F2 residue 310 LEU Chi-restraints excluded: chain F2 residue 344 GLU Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain F2 residue 369 TYR Chi-restraints excluded: chain L3 residue 13 ILE Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 72 THR Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 260 THR Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 297 HIS Chi-restraints excluded: chain F3 residue 310 LEU Chi-restraints excluded: chain F3 residue 342 GLU Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain L4 residue 12 SER Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain L4 residue 74 THR Chi-restraints excluded: chain L4 residue 89 LEU Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain F4 residue 40 VAL Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 132 SER Chi-restraints excluded: chain F4 residue 153 ILE Chi-restraints excluded: chain F4 residue 177 LEU Chi-restraints excluded: chain F4 residue 178 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 297 HIS Chi-restraints excluded: chain F4 residue 310 LEU Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 369 TYR Chi-restraints excluded: chain L5 residue 12 SER Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 74 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 19 CYS Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 100 MET Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 177 LEU Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 260 THR Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 297 HIS Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 344 GLU Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 36 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1 38 GLN L1 53 ASN H1 35 GLN ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 53 ASN ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 345 ASN ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 53 ASN ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L5 53 ASN ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.164836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.121010 restraints weight = 22561.587| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.36 r_work: 0.3020 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22240 Z= 0.106 Angle : 0.564 7.525 30320 Z= 0.287 Chirality : 0.043 0.138 3335 Planarity : 0.004 0.051 3905 Dihedral : 6.625 79.724 3054 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.38 % Allowed : 21.28 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.45 (0.15), residues: 2720 helix: -2.74 (0.34), residues: 160 sheet: -0.33 (0.20), residues: 680 loop : -2.18 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGF3 313 TYR 0.013 0.001 TYRH3 46 PHE 0.013 0.001 PHEF4 165 TRP 0.013 0.001 TRPH3 104 HIS 0.004 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00258 (22225) covalent geometry : angle 0.56408 (30290) SS BOND : bond 0.00112 ( 15) SS BOND : angle 0.73254 ( 30) hydrogen bonds : bond 0.02694 ( 560) hydrogen bonds : angle 5.00755 ( 1503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 290 time to evaluate : 0.977 Fit side-chains REVERT: H1 103 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7358 (t70) REVERT: F1 64 GLU cc_start: 0.7699 (tt0) cc_final: 0.7361 (tt0) REVERT: F1 103 LEU cc_start: 0.8341 (mt) cc_final: 0.7986 (mp) REVERT: F1 111 ASP cc_start: 0.6887 (t0) cc_final: 0.6421 (t0) REVERT: F2 103 LEU cc_start: 0.8599 (mt) cc_final: 0.8339 (mp) REVERT: F2 111 ASP cc_start: 0.7253 (t0) cc_final: 0.6693 (t0) REVERT: F2 235 GLU cc_start: 0.7259 (mp0) cc_final: 0.7026 (mp0) REVERT: F2 308 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8850 (mt) REVERT: F2 342 GLU cc_start: 0.7719 (mp0) cc_final: 0.6931 (mp0) REVERT: H3 36 VAL cc_start: 0.5891 (OUTLIER) cc_final: 0.5589 (p) REVERT: F3 111 ASP cc_start: 0.6929 (t0) cc_final: 0.6588 (t0) REVERT: F3 143 LYS cc_start: 0.8699 (tttt) cc_final: 0.8494 (ttpp) REVERT: F3 208 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8427 (tt) REVERT: F3 342 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: F4 111 ASP cc_start: 0.7256 (t0) cc_final: 0.6667 (t0) REVERT: F4 274 LYS cc_start: 0.8270 (mttp) cc_final: 0.8069 (mtpp) REVERT: F4 311 ARG cc_start: 0.8353 (ptt180) cc_final: 0.8151 (ptt180) REVERT: F5 103 LEU cc_start: 0.8438 (mt) cc_final: 0.8076 (mp) REVERT: F5 111 ASP cc_start: 0.7183 (t0) cc_final: 0.6682 (t0) REVERT: F5 208 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8678 (tt) REVERT: F5 219 ASP cc_start: 0.7840 (t0) cc_final: 0.7563 (t70) REVERT: F5 260 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8810 (t) outliers start: 106 outliers final: 71 residues processed: 371 average time/residue: 0.1320 time to fit residues: 80.5375 Evaluate side-chains 350 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 272 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 69 THR Chi-restraints excluded: chain L1 residue 89 LEU Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 57 ASP Chi-restraints excluded: chain H1 residue 103 ASP Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 76 SER Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 74 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 308 ILE Chi-restraints excluded: chain F2 residue 310 LEU Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain F2 residue 369 TYR Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 310 LEU Chi-restraints excluded: chain F3 residue 342 GLU Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 369 TYR Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain L4 residue 74 THR Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 132 SER Chi-restraints excluded: chain F4 residue 148 VAL Chi-restraints excluded: chain F4 residue 178 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 310 LEU Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain L5 residue 12 SER Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 74 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 28 LEU Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 100 MET Chi-restraints excluded: chain F5 residue 177 LEU Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 260 THR Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 147 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 35 optimal weight: 0.0020 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H1 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 92 ASN ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.162284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126464 restraints weight = 22364.712| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.18 r_work: 0.3011 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22240 Z= 0.163 Angle : 0.619 9.486 30320 Z= 0.310 Chirality : 0.044 0.146 3335 Planarity : 0.004 0.047 3905 Dihedral : 6.455 75.308 3036 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.79 % Allowed : 21.12 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.17 (0.16), residues: 2720 helix: -1.80 (0.46), residues: 120 sheet: -0.29 (0.18), residues: 795 loop : -2.09 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGF3 313 TYR 0.013 0.001 TYRH3 46 PHE 0.016 0.001 PHEF4 165 TRP 0.012 0.001 TRPH4 104 HIS 0.004 0.001 HISH2 31 Details of bonding type rmsd covalent geometry : bond 0.00402 (22225) covalent geometry : angle 0.61868 (30290) SS BOND : bond 0.00135 ( 15) SS BOND : angle 0.66473 ( 30) hydrogen bonds : bond 0.02903 ( 560) hydrogen bonds : angle 5.11220 ( 1503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 270 time to evaluate : 0.787 Fit side-chains REVERT: H1 103 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7274 (t70) REVERT: F1 64 GLU cc_start: 0.7817 (tt0) cc_final: 0.7476 (tt0) REVERT: F1 103 LEU cc_start: 0.8411 (mt) cc_final: 0.8066 (mp) REVERT: F1 111 ASP cc_start: 0.7020 (t0) cc_final: 0.6547 (t0) REVERT: L2 11 MET cc_start: 0.5948 (tpt) cc_final: 0.4376 (ttp) REVERT: F2 103 LEU cc_start: 0.8643 (mt) cc_final: 0.8389 (mp) REVERT: F2 111 ASP cc_start: 0.7291 (t0) cc_final: 0.6748 (t0) REVERT: F2 235 GLU cc_start: 0.7357 (mp0) cc_final: 0.7139 (mp0) REVERT: F2 308 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8932 (mt) REVERT: F2 342 GLU cc_start: 0.7785 (mp0) cc_final: 0.7035 (mp0) REVERT: H3 36 VAL cc_start: 0.6070 (OUTLIER) cc_final: 0.5781 (p) REVERT: F3 111 ASP cc_start: 0.7091 (t0) cc_final: 0.6645 (t0) REVERT: F3 143 LYS cc_start: 0.8835 (tttt) cc_final: 0.8603 (ttpp) REVERT: F3 208 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8500 (tt) REVERT: F3 260 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8947 (t) REVERT: F3 342 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: F4 111 ASP cc_start: 0.7420 (t0) cc_final: 0.6851 (t0) REVERT: F4 311 ARG cc_start: 0.8546 (ptt180) cc_final: 0.8279 (ptt180) REVERT: L5 95 PRO cc_start: 0.8410 (Cg_endo) cc_final: 0.8183 (Cg_exo) REVERT: F5 103 LEU cc_start: 0.8475 (mt) cc_final: 0.8138 (mp) REVERT: F5 111 ASP cc_start: 0.7456 (t0) cc_final: 0.7022 (t0) REVERT: F5 208 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8720 (tt) REVERT: F5 219 ASP cc_start: 0.7863 (t0) cc_final: 0.7656 (t70) REVERT: F5 260 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8893 (t) outliers start: 116 outliers final: 90 residues processed: 361 average time/residue: 0.1356 time to fit residues: 79.9417 Evaluate side-chains 358 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 260 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 21 MET Chi-restraints excluded: chain L1 residue 69 THR Chi-restraints excluded: chain H1 residue 24 THR Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 103 ASP Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 76 SER Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 148 VAL Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 225 GLU Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 297 HIS Chi-restraints excluded: chain F1 residue 332 MET Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain L2 residue 21 MET Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 74 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain H2 residue 49 SER Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 237 THR Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 308 ILE Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain F2 residue 369 TYR Chi-restraints excluded: chain L3 residue 13 ILE Chi-restraints excluded: chain L3 residue 21 MET Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 72 THR Chi-restraints excluded: chain L3 residue 74 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 260 THR Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 297 HIS Chi-restraints excluded: chain F3 residue 321 MET Chi-restraints excluded: chain F3 residue 342 GLU Chi-restraints excluded: chain F3 residue 352 ARG Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 369 TYR Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain L4 residue 74 THR Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 132 SER Chi-restraints excluded: chain F4 residue 148 VAL Chi-restraints excluded: chain F4 residue 178 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 310 LEU Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 369 TYR Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 74 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 100 MET Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 177 LEU Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 237 THR Chi-restraints excluded: chain F5 residue 260 THR Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 297 HIS Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 128 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 202 optimal weight: 0.0020 chunk 227 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 52 optimal weight: 0.3980 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H1 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 93 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 = 0.3691 r_free = 0.3691 target = 0.163106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.119583 restraints weight = 22519.465| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.37 r_work: 0.2985 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22240 Z= 0.129 Angle : 0.584 8.303 30320 Z= 0.295 Chirality : 0.043 0.143 3335 Planarity : 0.004 0.048 3905 Dihedral : 6.111 77.822 3032 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.55 % Allowed : 22.02 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.17 (0.16), residues: 2720 helix: -2.20 (0.39), residues: 160 sheet: -0.31 (0.19), residues: 715 loop : -1.96 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGF3 313 TYR 0.012 0.001 TYRH3 46 PHE 0.014 0.001 PHEF4 165 TRP 0.013 0.001 TRPH4 104 HIS 0.004 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00317 (22225) covalent geometry : angle 0.58442 (30290) SS BOND : bond 0.00093 ( 15) SS BOND : angle 0.65232 ( 30) hydrogen bonds : bond 0.02779 ( 560) hydrogen bonds : angle 4.96827 ( 1503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 261 time to evaluate : 0.779 Fit side-chains REVERT: H1 103 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7215 (t70) REVERT: F1 64 GLU cc_start: 0.7741 (tt0) cc_final: 0.7416 (tt0) REVERT: F1 103 LEU cc_start: 0.8339 (mt) cc_final: 0.7974 (mp) REVERT: F1 111 ASP cc_start: 0.6906 (t0) cc_final: 0.6500 (t0) REVERT: L2 11 MET cc_start: 0.6037 (tpt) cc_final: 0.4362 (ttp) REVERT: F2 103 LEU cc_start: 0.8603 (mt) cc_final: 0.8344 (mp) REVERT: F2 111 ASP cc_start: 0.7088 (t0) cc_final: 0.6565 (t0) REVERT: F2 170 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8047 (mt-10) REVERT: F2 235 GLU cc_start: 0.7292 (mp0) cc_final: 0.7049 (mp0) REVERT: F2 289 ARG cc_start: 0.8680 (ttt180) cc_final: 0.8413 (ttt180) REVERT: F2 308 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8894 (mt) REVERT: H3 36 VAL cc_start: 0.5924 (OUTLIER) cc_final: 0.5624 (p) REVERT: F3 111 ASP cc_start: 0.7001 (t0) cc_final: 0.6575 (t0) REVERT: F3 143 LYS cc_start: 0.8741 (tttt) cc_final: 0.8487 (ttpp) REVERT: F3 208 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8517 (tt) REVERT: F3 219 ASP cc_start: 0.8055 (t0) cc_final: 0.7805 (t70) REVERT: F3 342 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: F4 111 ASP cc_start: 0.7210 (t0) cc_final: 0.6667 (t0) REVERT: L5 11 MET cc_start: 0.6098 (tpt) cc_final: 0.4750 (ttp) REVERT: L5 95 PRO cc_start: 0.8353 (Cg_endo) cc_final: 0.8138 (Cg_exo) REVERT: F5 111 ASP cc_start: 0.7219 (t0) cc_final: 0.6784 (t0) REVERT: F5 208 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (tt) REVERT: F5 219 ASP cc_start: 0.7852 (t0) cc_final: 0.7568 (t70) REVERT: F5 260 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8916 (t) REVERT: F5 352 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8378 (mtp85) outliers start: 110 outliers final: 83 residues processed: 347 average time/residue: 0.1347 time to fit residues: 76.4142 Evaluate side-chains 347 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 256 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 21 MET Chi-restraints excluded: chain L1 residue 69 THR Chi-restraints excluded: chain L1 residue 89 LEU Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 103 ASP Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 76 SER Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 148 VAL Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 260 THR Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 297 HIS Chi-restraints excluded: chain F1 residue 344 GLU Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain H2 residue 49 SER Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 148 VAL Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 237 THR Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 308 ILE Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain F2 residue 369 TYR Chi-restraints excluded: chain L3 residue 13 ILE Chi-restraints excluded: chain L3 residue 21 MET Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 187 GLU Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 297 HIS Chi-restraints excluded: chain F3 residue 321 MET Chi-restraints excluded: chain F3 residue 342 GLU Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 369 TYR Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain L4 residue 74 THR Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 132 SER Chi-restraints excluded: chain F4 residue 148 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 297 HIS Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain L5 residue 21 MET Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 74 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 100 MET Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 148 VAL Chi-restraints excluded: chain F5 residue 177 LEU Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 260 THR Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 297 HIS Chi-restraints excluded: chain F5 residue 352 ARG Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 84 optimal weight: 0.2980 chunk 193 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 0.0020 chunk 137 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H1 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 163 HIS L3 53 ASN ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 71 GLN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.168083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.135749 restraints weight = 22259.345| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.14 r_work: 0.3114 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22240 Z= 0.095 Angle : 0.543 6.708 30320 Z= 0.276 Chirality : 0.042 0.140 3335 Planarity : 0.004 0.046 3905 Dihedral : 5.503 80.409 3026 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.64 % Allowed : 23.06 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.83 (0.16), residues: 2720 helix: -1.14 (0.49), residues: 125 sheet: -0.22 (0.19), residues: 720 loop : -1.74 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGF3 313 TYR 0.011 0.001 TYRH3 46 PHE 0.012 0.001 PHEF4 165 TRP 0.012 0.001 TRPH1 104 HIS 0.003 0.001 HISF3 298 Details of bonding type rmsd covalent geometry : bond 0.00231 (22225) covalent geometry : angle 0.54263 (30290) SS BOND : bond 0.00117 ( 15) SS BOND : angle 0.47192 ( 30) hydrogen bonds : bond 0.02579 ( 560) hydrogen bonds : angle 4.69182 ( 1503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 298 time to evaluate : 0.865 Fit side-chains REVERT: H1 27 SER cc_start: 0.8199 (m) cc_final: 0.7771 (t) REVERT: H1 103 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7246 (t70) REVERT: F1 64 GLU cc_start: 0.7482 (tt0) cc_final: 0.7168 (tt0) REVERT: F1 87 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6961 (mm-30) REVERT: F1 103 LEU cc_start: 0.8282 (mt) cc_final: 0.7913 (mp) REVERT: L2 11 MET cc_start: 0.6007 (tpt) cc_final: 0.4283 (ttp) REVERT: F2 111 ASP cc_start: 0.6763 (t0) cc_final: 0.6365 (t0) REVERT: F2 289 ARG cc_start: 0.8622 (ttt180) cc_final: 0.8371 (ttt180) REVERT: F2 342 GLU cc_start: 0.7601 (mp0) cc_final: 0.7372 (mt-10) REVERT: H3 36 VAL cc_start: 0.5891 (OUTLIER) cc_final: 0.5621 (p) REVERT: F3 111 ASP cc_start: 0.6507 (t0) cc_final: 0.6303 (t0) REVERT: F3 219 ASP cc_start: 0.7878 (t0) cc_final: 0.7584 (t70) REVERT: F3 235 GLU cc_start: 0.6937 (mp0) cc_final: 0.6638 (mp0) REVERT: F3 259 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7963 (mt) REVERT: F3 260 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8942 (t) REVERT: F3 332 MET cc_start: 0.6213 (ptp) cc_final: 0.5947 (ptp) REVERT: F3 342 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: F4 111 ASP cc_start: 0.6874 (t0) cc_final: 0.6469 (t0) REVERT: F5 111 ASP cc_start: 0.6889 (t0) cc_final: 0.6610 (t0) REVERT: F5 208 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8605 (tt) REVERT: F5 219 ASP cc_start: 0.7619 (t0) cc_final: 0.7296 (t70) REVERT: F5 257 ASN cc_start: 0.8261 (t0) cc_final: 0.7652 (t0) REVERT: F5 260 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8884 (t) REVERT: F5 352 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8351 (mtp85) outliers start: 88 outliers final: 64 residues processed: 366 average time/residue: 0.1335 time to fit residues: 78.7532 Evaluate side-chains 351 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 279 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 21 MET Chi-restraints excluded: chain L1 residue 69 THR Chi-restraints excluded: chain L1 residue 89 LEU Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 103 ASP Chi-restraints excluded: chain F1 residue 62 THR Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 148 VAL Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 260 THR Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 148 VAL Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain L3 residue 13 ILE Chi-restraints excluded: chain L3 residue 21 MET Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 72 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 148 VAL Chi-restraints excluded: chain F3 residue 187 GLU Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 260 THR Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 342 GLU Chi-restraints excluded: chain F3 residue 352 ARG Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 369 TYR Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 148 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 148 VAL Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 260 THR Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 352 ARG Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 28 optimal weight: 10.0000 chunk 73 optimal weight: 0.0270 chunk 111 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 149 optimal weight: 0.4980 chunk 106 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 overall best weight: 3.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H1 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 109 ASN F1 118 GLN ** F1 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 92 ASN ** F3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 109 ASN F3 118 GLN ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 118 GLN ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 92 ASN ** F5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.159492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123371 restraints weight = 22438.690| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.22 r_work: 0.2942 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22240 Z= 0.257 Angle : 0.712 11.585 30320 Z= 0.354 Chirality : 0.048 0.173 3335 Planarity : 0.005 0.049 3905 Dihedral : 6.133 71.409 3015 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.68 % Allowed : 23.47 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.86 (0.16), residues: 2720 helix: -1.50 (0.51), residues: 120 sheet: -0.07 (0.19), residues: 780 loop : -1.87 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGF3 313 TYR 0.022 0.002 TYRF3 72 PHE 0.019 0.002 PHEF4 165 TRP 0.012 0.002 TRPH4 104 HIS 0.005 0.002 HISH3 31 Details of bonding type rmsd covalent geometry : bond 0.00639 (22225) covalent geometry : angle 0.71176 (30290) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.77876 ( 30) hydrogen bonds : bond 0.03230 ( 560) hydrogen bonds : angle 5.25958 ( 1503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 273 time to evaluate : 0.772 Fit side-chains REVERT: L1 11 MET cc_start: 0.5959 (tpt) cc_final: 0.5258 (ttp) REVERT: H1 103 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7176 (t70) REVERT: F1 64 GLU cc_start: 0.7682 (tt0) cc_final: 0.7358 (tt0) REVERT: F1 87 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7173 (mm-30) REVERT: F1 103 LEU cc_start: 0.8418 (mt) cc_final: 0.8068 (mp) REVERT: F2 103 LEU cc_start: 0.8645 (mt) cc_final: 0.8382 (mp) REVERT: F2 111 ASP cc_start: 0.7132 (t0) cc_final: 0.6596 (t0) REVERT: F2 308 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8911 (mt) REVERT: F2 342 GLU cc_start: 0.7756 (mp0) cc_final: 0.7465 (mt-10) REVERT: L3 95 PRO cc_start: 0.8221 (Cg_endo) cc_final: 0.8020 (Cg_exo) REVERT: H3 36 VAL cc_start: 0.5872 (OUTLIER) cc_final: 0.5596 (p) REVERT: F3 111 ASP cc_start: 0.7357 (t0) cc_final: 0.6937 (t0) REVERT: F3 260 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8983 (t) REVERT: F3 342 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: F4 111 ASP cc_start: 0.7451 (t0) cc_final: 0.6870 (t0) REVERT: L5 11 MET cc_start: 0.6043 (tpt) cc_final: 0.4735 (ttp) REVERT: L5 95 PRO cc_start: 0.8380 (Cg_endo) cc_final: 0.8141 (Cg_exo) REVERT: F5 103 LEU cc_start: 0.8485 (mt) cc_final: 0.8131 (mp) REVERT: F5 111 ASP cc_start: 0.7267 (t0) cc_final: 0.6868 (t0) REVERT: F5 208 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8755 (tt) REVERT: F5 260 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8906 (t) REVERT: F5 352 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8359 (mtp85) outliers start: 89 outliers final: 75 residues processed: 340 average time/residue: 0.1382 time to fit residues: 76.1597 Evaluate side-chains 344 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 261 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 21 MET Chi-restraints excluded: chain H1 residue 24 THR Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 57 ASP Chi-restraints excluded: chain H1 residue 103 ASP Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 148 VAL Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 225 GLU Chi-restraints excluded: chain F1 residue 260 THR Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 297 HIS Chi-restraints excluded: chain F1 residue 344 GLU Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain L2 residue 21 MET Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain H2 residue 49 SER Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 148 VAL Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 308 ILE Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain F2 residue 369 TYR Chi-restraints excluded: chain L3 residue 13 ILE Chi-restraints excluded: chain L3 residue 21 MET Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 72 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 148 VAL Chi-restraints excluded: chain F3 residue 187 GLU Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 260 THR Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 342 GLU Chi-restraints excluded: chain F3 residue 352 ARG Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 369 TYR Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 148 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 297 HIS Chi-restraints excluded: chain F4 residue 321 MET Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 369 TYR Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 148 VAL Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 207 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 260 THR Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 297 HIS Chi-restraints excluded: chain F5 residue 352 ARG Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 210 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H1 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 93 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 = 0.3709 r_free = 0.3709 target = 0.164421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.131346 restraints weight = 22332.900| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.15 r_work: 0.3015 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22240 Z= 0.139 Angle : 0.610 9.012 30320 Z= 0.307 Chirality : 0.044 0.145 3335 Planarity : 0.004 0.051 3905 Dihedral : 5.574 40.338 3012 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.35 % Allowed : 23.97 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.82 (0.16), residues: 2720 helix: -2.08 (0.40), residues: 160 sheet: -0.00 (0.19), residues: 780 loop : -1.79 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGF3 313 TYR 0.012 0.001 TYRH3 46 PHE 0.015 0.001 PHEF3 165 TRP 0.014 0.001 TRPH3 104 HIS 0.003 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00341 (22225) covalent geometry : angle 0.61010 (30290) SS BOND : bond 0.00112 ( 15) SS BOND : angle 0.52953 ( 30) hydrogen bonds : bond 0.02857 ( 560) hydrogen bonds : angle 5.01419 ( 1503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 260 time to evaluate : 0.759 Fit side-chains REVERT: L1 11 MET cc_start: 0.6043 (tpt) cc_final: 0.5250 (ttp) REVERT: H1 103 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7111 (t70) REVERT: F1 64 GLU cc_start: 0.7619 (tt0) cc_final: 0.7302 (tt0) REVERT: F1 87 GLU cc_start: 0.7242 (mm-30) cc_final: 0.7025 (mm-30) REVERT: F1 103 LEU cc_start: 0.8312 (mt) cc_final: 0.7938 (mp) REVERT: L2 11 MET cc_start: 0.6099 (tpt) cc_final: 0.4381 (ttp) REVERT: F2 103 LEU cc_start: 0.8593 (mt) cc_final: 0.8320 (mp) REVERT: F2 111 ASP cc_start: 0.7047 (t0) cc_final: 0.6566 (t0) REVERT: F2 170 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7788 (mt-10) REVERT: F2 289 ARG cc_start: 0.8635 (ttt180) cc_final: 0.8366 (ttt180) REVERT: H3 36 VAL cc_start: 0.5821 (OUTLIER) cc_final: 0.5525 (p) REVERT: F3 111 ASP cc_start: 0.7072 (t0) cc_final: 0.6778 (t0) REVERT: F3 260 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8925 (t) REVERT: F3 342 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: F4 111 ASP cc_start: 0.7196 (t0) cc_final: 0.6702 (t0) REVERT: L5 11 MET cc_start: 0.6058 (tpt) cc_final: 0.4734 (ttp) REVERT: L5 95 PRO cc_start: 0.8324 (Cg_endo) cc_final: 0.8112 (Cg_exo) REVERT: F5 111 ASP cc_start: 0.7204 (t0) cc_final: 0.6814 (t0) REVERT: F5 208 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8686 (tt) REVERT: F5 260 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8896 (t) REVERT: F5 352 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8331 (mtp85) outliers start: 81 outliers final: 71 residues processed: 321 average time/residue: 0.1384 time to fit residues: 72.3761 Evaluate side-chains 333 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 255 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L1 residue 21 MET Chi-restraints excluded: chain H1 residue 24 THR Chi-restraints excluded: chain H1 residue 36 VAL Chi-restraints excluded: chain H1 residue 103 ASP Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 76 SER Chi-restraints excluded: chain F1 residue 100 MET Chi-restraints excluded: chain F1 residue 132 SER Chi-restraints excluded: chain F1 residue 148 VAL Chi-restraints excluded: chain F1 residue 190 VAL Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 208 LEU Chi-restraints excluded: chain F1 residue 260 THR Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 352 ARG Chi-restraints excluded: chain F1 residue 365 ASP Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain L2 residue 21 MET Chi-restraints excluded: chain L2 residue 69 THR Chi-restraints excluded: chain L2 residue 85 VAL Chi-restraints excluded: chain H2 residue 24 THR Chi-restraints excluded: chain H2 residue 36 VAL Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 100 MET Chi-restraints excluded: chain F2 residue 148 VAL Chi-restraints excluded: chain F2 residue 177 LEU Chi-restraints excluded: chain F2 residue 190 VAL Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 237 THR Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 365 ASP Chi-restraints excluded: chain L3 residue 13 ILE Chi-restraints excluded: chain L3 residue 21 MET Chi-restraints excluded: chain L3 residue 69 THR Chi-restraints excluded: chain L3 residue 72 THR Chi-restraints excluded: chain L3 residue 85 VAL Chi-restraints excluded: chain H3 residue 24 THR Chi-restraints excluded: chain H3 residue 36 VAL Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 148 VAL Chi-restraints excluded: chain F3 residue 187 GLU Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 260 THR Chi-restraints excluded: chain F3 residue 296 VAL Chi-restraints excluded: chain F3 residue 297 HIS Chi-restraints excluded: chain F3 residue 342 GLU Chi-restraints excluded: chain F3 residue 352 ARG Chi-restraints excluded: chain F3 residue 365 ASP Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 369 TYR Chi-restraints excluded: chain L4 residue 21 MET Chi-restraints excluded: chain L4 residue 69 THR Chi-restraints excluded: chain H4 residue 36 VAL Chi-restraints excluded: chain H4 residue 57 ASP Chi-restraints excluded: chain F4 residue 100 MET Chi-restraints excluded: chain F4 residue 148 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 365 ASP Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 369 TYR Chi-restraints excluded: chain L5 residue 69 THR Chi-restraints excluded: chain L5 residue 89 LEU Chi-restraints excluded: chain H5 residue 24 THR Chi-restraints excluded: chain H5 residue 36 VAL Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 132 SER Chi-restraints excluded: chain F5 residue 148 VAL Chi-restraints excluded: chain F5 residue 190 VAL Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 260 THR Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 352 ARG Chi-restraints excluded: chain F5 residue 365 ASP Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 369 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 181 optimal weight: 0.3980 chunk 53 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 143 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H1 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 71 GLN ** F3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.162603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.121825 restraints weight = 22628.020| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.38 r_work: 0.2991 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22240 Z= 0.134 Angle : 0.599 8.724 30320 Z= 0.302 Chirality : 0.044 0.146 3335 Planarity : 0.004 0.051 3905 Dihedral : 5.472 39.400 3012 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 3.64 % Allowed : 23.64 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.84 (0.16), residues: 2720 helix: -2.02 (0.41), residues: 160 sheet: -0.08 (0.20), residues: 705 loop : -1.71 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGF3 313 TYR 0.011 0.001 TYRH3 46 PHE 0.014 0.001 PHEF4 165 TRP 0.012 0.001 TRPH4 104 HIS 0.004 0.001 HISH2 31 Details of bonding type rmsd covalent geometry : bond 0.00328 (22225) covalent geometry : angle 0.59895 (30290) SS BOND : bond 0.00098 ( 15) SS BOND : angle 0.49563 ( 30) hydrogen bonds : bond 0.02809 ( 560) hydrogen bonds : angle 4.91470 ( 1503) =============================================================================== Job complete usr+sys time: 5762.15 seconds wall clock time: 99 minutes 29.79 seconds (5969.79 seconds total)