Starting phenix.real_space_refine on Thu Feb 5 11:32:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtj_48611/02_2026/9mtj_48611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtj_48611/02_2026/9mtj_48611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mtj_48611/02_2026/9mtj_48611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtj_48611/02_2026/9mtj_48611.map" model { file = "/net/cci-nas-00/data/ceres_data/9mtj_48611/02_2026/9mtj_48611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtj_48611/02_2026/9mtj_48611.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 74 5.16 5 C 10578 2.51 5 N 2898 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16805 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2512 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 301} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1360 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2508 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 301} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "E" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2508 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 301} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 947 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 929 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "J" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 789 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 789 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 98} Time building chain proxies: 3.63, per 1000 atoms: 0.22 Number of scatterers: 16805 At special positions: 0 Unit cell: (132.25, 140.714, 147.062, 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 74 16.00 O 3255 8.00 N 2898 7.00 C 10578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.06 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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: 1.16 Conformation dependent library (CDL) restraints added in 744.3 milliseconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3950 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 54 sheets defined 20.5% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.896A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.589A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.894A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.762A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.821A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.580A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.560A pdb=" N LYS F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.793A pdb=" N GLU F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 170 removed outlier: 3.781A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.504A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.629A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.943A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.645A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.528A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.710A pdb=" N THR M 87 " --> pdb=" O THR M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.643A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.235A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.563A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.493A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 121A removed outlier: 6.282A pdb=" N SER A 260A" --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 118 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.509A pdb=" N SER A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER A 138 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N GLU A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.749A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.141A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR C 28 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS C 32 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 53A removed outlier: 5.371A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.424A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 121A removed outlier: 6.342A pdb=" N SER C 260A" --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE C 118 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA C 259 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG C 120 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 257 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.466A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.828A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 64 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 31 through 36 removed outlier: 5.984A pdb=" N CYS F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.123A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 53 removed outlier: 5.229A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.294A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 117 through 121A removed outlier: 6.636A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.716A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.523A pdb=" N ILE E 288 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.724A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.844A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.918A pdb=" N GLY I 10 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.918A pdb=" N GLY I 10 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AE8, first strand: chain 'J' and resid 8 through 12 removed outlier: 6.157A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 8 through 12 Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AF2, first strand: chain 'L' and resid 8 through 12 removed outlier: 6.070A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 8 through 12 Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.701A pdb=" N ILE M 34 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.003A pdb=" N LEU M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'N' and resid 8 through 13 removed outlier: 5.993A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 8 through 13 710 hydrogen bonds defined for protein. 1869 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: 3.02 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5588 1.35 - 1.48: 4414 1.48 - 1.61: 7096 1.61 - 1.74: 0 1.74 - 1.87: 103 Bond restraints: 17201 Sorted by residual: bond pdb=" C ARG E 211 " pdb=" N LYS E 212 " ideal model delta sigma weight residual 1.331 1.247 0.084 1.32e-02 5.74e+03 4.02e+01 bond pdb=" C LYS A 212 " pdb=" N PHE A 213 " ideal model delta sigma weight residual 1.330 1.262 0.068 1.39e-02 5.18e+03 2.38e+01 bond pdb=" C ARG A 211 " pdb=" N LYS A 212 " ideal model delta sigma weight residual 1.332 1.269 0.062 1.35e-02 5.49e+03 2.13e+01 bond pdb=" CA SER B 124 " pdb=" CB SER B 124 " ideal model delta sigma weight residual 1.529 1.461 0.068 1.58e-02 4.01e+03 1.84e+01 bond pdb=" CA SER J 94 " pdb=" CB SER J 94 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.58e-02 4.01e+03 1.43e+01 ... (remaining 17196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 22865 2.33 - 4.66: 410 4.66 - 6.98: 52 6.98 - 9.31: 11 9.31 - 11.64: 3 Bond angle restraints: 23341 Sorted by residual: angle pdb=" C PRO J 95 " pdb=" CA PRO J 95 " pdb=" CB PRO J 95 " ideal model delta sigma weight residual 111.56 122.68 -11.12 1.65e+00 3.67e-01 4.54e+01 angle pdb=" C LYS A 197 " pdb=" CA LYS A 197 " pdb=" CB LYS A 197 " ideal model delta sigma weight residual 110.03 100.81 9.22 1.72e+00 3.38e-01 2.87e+01 angle pdb=" C LYS E 197 " pdb=" CA LYS E 197 " pdb=" CB LYS E 197 " ideal model delta sigma weight residual 110.95 101.66 9.29 1.80e+00 3.09e-01 2.66e+01 angle pdb=" N ARG E 192 " pdb=" CA ARG E 192 " pdb=" CB ARG E 192 " ideal model delta sigma weight residual 110.40 102.08 8.32 1.63e+00 3.76e-01 2.60e+01 angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 112.72 106.97 5.75 1.14e+00 7.69e-01 2.54e+01 ... (remaining 23336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8814 17.78 - 35.55: 995 35.55 - 53.33: 302 53.33 - 71.10: 74 71.10 - 88.88: 18 Dihedral angle restraints: 10203 sinusoidal: 3999 harmonic: 6204 Sorted by residual: dihedral pdb=" CD ARG M 96 " pdb=" NE ARG M 96 " pdb=" CZ ARG M 96 " pdb=" NH1 ARG M 96 " ideal model delta sinusoidal sigma weight residual 0.00 -75.45 75.45 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " pdb=" NH1 ARG A 192 " ideal model delta sinusoidal sigma weight residual 0.00 -65.21 65.21 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CD ARG I 96 " pdb=" NE ARG I 96 " pdb=" CZ ARG I 96 " pdb=" NH1 ARG I 96 " ideal model delta sinusoidal sigma weight residual 0.00 52.77 -52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 10200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2231 0.075 - 0.150: 263 0.150 - 0.225: 21 0.225 - 0.300: 6 0.300 - 0.376: 2 Chirality restraints: 2523 Sorted by residual: chirality pdb=" CA LEU B 126 " pdb=" N LEU B 126 " pdb=" C LEU B 126 " pdb=" CB LEU B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA LYS A 197 " pdb=" N LYS A 197 " pdb=" C LYS A 197 " pdb=" CB LYS A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA LYS E 197 " pdb=" N LYS E 197 " pdb=" C LYS E 197 " pdb=" CB LYS E 197 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2520 not shown) Planarity restraints: 3044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 96 " 1.071 9.50e-02 1.11e+02 4.80e-01 1.39e+02 pdb=" NE ARG M 96 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG M 96 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG M 96 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG M 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.990 9.50e-02 1.11e+02 4.44e-01 1.19e+02 pdb=" NE ARG A 192 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 96 " -0.865 9.50e-02 1.11e+02 3.88e-01 9.13e+01 pdb=" NE ARG I 96 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG I 96 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG I 96 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 96 " -0.024 2.00e-02 2.50e+03 ... (remaining 3041 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2047 2.75 - 3.29: 14831 3.29 - 3.82: 28216 3.82 - 4.36: 34053 4.36 - 4.90: 60335 Nonbonded interactions: 139482 Sorted by model distance: nonbonded pdb=" O LYS F 39 " pdb=" ND2 ASN F 43 " model vdw 2.212 3.120 nonbonded pdb=" OE2 GLU A 216 " pdb=" NH2 ARG A 220 " model vdw 2.215 3.120 nonbonded pdb=" OE1 GLN A 111 " pdb=" NH1 ARG A 261 " model vdw 2.232 3.120 nonbonded pdb=" O PRO A 122 " pdb=" OG SER A 126 " model vdw 2.245 3.040 nonbonded pdb=" O SER H 82B" pdb=" OG SER H 82B" model vdw 2.251 3.040 ... (remaining 139477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 76 or (resid 77 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 123 or (resid 124 and ( \ name N or name CA or name C or name O or name CB )) or resid 125 through 148 or \ (resid 149 and (name N or name CA or name C or name O or name CB )) or resid 150 \ through 226 or (resid 227 and (name N or name CA or name C or name O or name CB \ )) or resid 228 through 273 or (resid 274 and (name N or name CA or name C or n \ ame O or name CB )) or resid 275 through 325)) selection = (chain 'C' and (resid 11 through 123 or (resid 124 and (name N or name CA or nam \ e C or name O or name CB )) or resid 125 through 226 or (resid 227 and (name N o \ r name CA or name C or name O or name CB )) or resid 228 through 237 or (resid 2 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 239 through \ 273 or (resid 274 and (name N or name CA or name C or name O or name CB )) or r \ esid 275 through 325)) selection = (chain 'E' and (resid 11 through 76 or (resid 77 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 148 or (resid 149 and ( \ name N or name CA or name C or name O or name CB )) or resid 150 through 237 or \ (resid 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 325)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 2 through 163 or (resid 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 170)) selection = (chain 'F' and (resid 2 through 163 or (resid 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 170)) } ncs_group { reference = (chain 'H' and resid 3 through 113) selection = chain 'I' selection = (chain 'M' and resid 3 through 113) } ncs_group { reference = chain 'J' selection = chain 'L' selection = (chain 'N' and resid 3 through 106) } 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: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.050 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.005 0.084 17219 Z= 0.267 Angle : 0.719 11.640 23377 Z= 0.426 Chirality : 0.049 0.376 2523 Planarity : 0.018 0.480 3044 Dihedral : 17.045 88.877 6199 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.52 % Favored : 97.29 % Rotamer: Outliers : 1.69 % Allowed : 22.61 % Favored : 75.70 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2143 helix: 2.34 (0.27), residues: 351 sheet: 1.52 (0.25), residues: 443 loop : -0.66 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.015 0.001 TYR C 201 PHE 0.012 0.001 PHE D 140 TRP 0.006 0.001 TRP I 103 HIS 0.007 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00471 (17201) covalent geometry : angle 0.71581 (23341) SS BOND : bond 0.00848 ( 18) SS BOND : angle 1.77528 ( 36) hydrogen bonds : bond 0.18052 ( 681) hydrogen bonds : angle 7.51787 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 403 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7131 (pt0) cc_final: 0.6340 (mt-10) REVERT: A 161 TYR cc_start: 0.9199 (t80) cc_final: 0.8880 (t80) REVERT: A 295 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: A 296 ASN cc_start: 0.8376 (p0) cc_final: 0.7987 (p0) REVERT: B 132 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7418 (mt-10) REVERT: C 75 GLU cc_start: 0.7002 (pt0) cc_final: 0.6782 (pt0) REVERT: E 194 LEU cc_start: 0.8552 (mt) cc_final: 0.8311 (mp) REVERT: N 89 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8478 (t0) outliers start: 31 outliers final: 15 residues processed: 425 average time/residue: 0.7138 time to fit residues: 329.7689 Evaluate side-chains 406 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 389 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 96 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 89 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 269 ASN A 295 GLN B 154 ASN D 43 ASN E 295 GLN F 125 GLN F 154 ASN F 169 ASN H 76 ASN I 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099116 restraints weight = 23888.242| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.65 r_work: 0.3231 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17219 Z= 0.158 Angle : 0.568 14.261 23377 Z= 0.293 Chirality : 0.044 0.228 2523 Planarity : 0.006 0.157 3044 Dihedral : 5.497 56.179 2373 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.24 % Favored : 97.57 % Rotamer: Outliers : 3.60 % Allowed : 20.15 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2143 helix: 2.34 (0.27), residues: 369 sheet: 1.41 (0.23), residues: 469 loop : -0.53 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 96 TYR 0.015 0.001 TYR E 195 PHE 0.013 0.001 PHE J 36 TRP 0.009 0.001 TRP L 35 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00372 (17201) covalent geometry : angle 0.56728 (23341) SS BOND : bond 0.00384 ( 18) SS BOND : angle 0.82153 ( 36) hydrogen bonds : bond 0.04852 ( 681) hydrogen bonds : angle 5.40062 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 414 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7221 (pt0) cc_final: 0.6619 (mt-10) REVERT: A 161 TYR cc_start: 0.9003 (t80) cc_final: 0.8748 (t80) REVERT: A 187 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7877 (p0) REVERT: A 220 ARG cc_start: 0.8532 (mtm180) cc_final: 0.8303 (mtm180) REVERT: B 27 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8213 (tt0) outliers start: 66 outliers final: 37 residues processed: 446 average time/residue: 0.6194 time to fit residues: 302.1858 Evaluate side-chains 441 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 402 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 70 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 269 ASN B 125 GLN B 154 ASN D 43 ASN D 53 ASN E 111 GLN E 158 ASN E 295 GLN F 125 GLN F 154 ASN F 169 ASN H 76 ASN I 76 ASN J 69 ASN N 89 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096971 restraints weight = 24040.102| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.65 r_work: 0.3185 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.151 17219 Z= 0.407 Angle : 0.705 10.862 23377 Z= 0.360 Chirality : 0.051 0.239 2523 Planarity : 0.006 0.146 3044 Dihedral : 5.479 57.906 2351 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.66 % Favored : 97.11 % Rotamer: Outliers : 4.75 % Allowed : 18.95 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2143 helix: 1.71 (0.27), residues: 378 sheet: 1.20 (0.23), residues: 482 loop : -0.68 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 81A TYR 0.017 0.002 TYR E 195 PHE 0.020 0.003 PHE I 67 TRP 0.012 0.002 TRP H 36 HIS 0.009 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00983 (17201) covalent geometry : angle 0.70442 (23341) SS BOND : bond 0.00515 ( 18) SS BOND : angle 1.14811 ( 36) hydrogen bonds : bond 0.05731 ( 681) hydrogen bonds : angle 5.41464 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 399 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7135 (pt0) cc_final: 0.6720 (mt-10) REVERT: A 106 GLU cc_start: 0.8197 (mp0) cc_final: 0.7962 (mp0) REVERT: A 187 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 27 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: B 132 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 31 GLU cc_start: 0.8148 (tt0) cc_final: 0.7904 (tt0) REVERT: M 70 SER cc_start: 0.8588 (m) cc_final: 0.8382 (t) REVERT: N 103 HIS cc_start: 0.8272 (t-90) cc_final: 0.7885 (t-90) outliers start: 87 outliers final: 56 residues processed: 452 average time/residue: 0.6110 time to fit residues: 302.8739 Evaluate side-chains 448 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 390 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 269 ASN B 125 GLN B 128 ASN B 154 ASN C 226 GLN D 43 ASN D 125 GLN D 154 ASN E 111 GLN E 226 GLN E 295 GLN F 43 ASN F 125 GLN F 154 ASN F 169 ASN H 76 ASN I 76 ASN M 76 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098592 restraints weight = 23853.941| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.64 r_work: 0.3211 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17219 Z= 0.169 Angle : 0.564 9.579 23377 Z= 0.294 Chirality : 0.044 0.223 2523 Planarity : 0.005 0.134 3044 Dihedral : 5.043 55.972 2351 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.15 % Favored : 97.67 % Rotamer: Outliers : 3.88 % Allowed : 19.93 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2143 helix: 2.06 (0.27), residues: 372 sheet: 1.27 (0.23), residues: 472 loop : -0.61 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 81A TYR 0.015 0.001 TYR A 161 PHE 0.011 0.001 PHE J 36 TRP 0.009 0.001 TRP L 35 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00405 (17201) covalent geometry : angle 0.56315 (23341) SS BOND : bond 0.00283 ( 18) SS BOND : angle 0.97765 ( 36) hydrogen bonds : bond 0.04599 ( 681) hydrogen bonds : angle 5.10547 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 399 time to evaluate : 0.839 Fit side-chains REVERT: A 75 GLU cc_start: 0.7099 (pt0) cc_final: 0.6734 (mt-10) REVERT: A 187 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7873 (p0) REVERT: B 27 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 132 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 220 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6924 (mtm180) REVERT: C 274 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7280 (tpt) REVERT: D 105 GLU cc_start: 0.7642 (tp30) cc_final: 0.7401 (tp30) REVERT: E 77 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: E 106 GLU cc_start: 0.7991 (mp0) cc_final: 0.7575 (mp0) REVERT: F 43 ASN cc_start: 0.8443 (m-40) cc_final: 0.8177 (m-40) REVERT: M 70 SER cc_start: 0.8551 (m) cc_final: 0.8337 (t) REVERT: M 82 MET cc_start: 0.8675 (mtp) cc_final: 0.8422 (mtp) REVERT: N 103 HIS cc_start: 0.8272 (t-90) cc_final: 0.7853 (t-90) outliers start: 71 outliers final: 41 residues processed: 434 average time/residue: 0.5966 time to fit residues: 283.7150 Evaluate side-chains 441 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 395 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 208 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 189 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 269 ASN B 53 ASN B 125 GLN B 154 ASN D 43 ASN E 111 GLN E 226 GLN E 295 GLN F 125 GLN F 154 ASN F 169 ASN H 76 ASN I 76 ASN M 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098369 restraints weight = 23638.949| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.64 r_work: 0.3209 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 17219 Z= 0.200 Angle : 0.572 9.993 23377 Z= 0.296 Chirality : 0.044 0.231 2523 Planarity : 0.005 0.129 3044 Dihedral : 4.986 58.449 2347 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.47 % Favored : 97.34 % Rotamer: Outliers : 4.31 % Allowed : 19.55 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2143 helix: 2.12 (0.27), residues: 372 sheet: 1.25 (0.23), residues: 472 loop : -0.61 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 71 TYR 0.014 0.002 TYR A 161 PHE 0.011 0.002 PHE F 110 TRP 0.009 0.001 TRP L 35 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00485 (17201) covalent geometry : angle 0.57100 (23341) SS BOND : bond 0.00362 ( 18) SS BOND : angle 1.09188 ( 36) hydrogen bonds : bond 0.04620 ( 681) hydrogen bonds : angle 5.01902 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 387 time to evaluate : 0.429 Fit side-chains REVERT: A 75 GLU cc_start: 0.7173 (pt0) cc_final: 0.6796 (mt-10) REVERT: A 106 GLU cc_start: 0.8205 (mp0) cc_final: 0.7957 (mp0) REVERT: A 187 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7888 (p0) REVERT: B 27 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: B 103 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 105 GLU cc_start: 0.7847 (tp30) cc_final: 0.7539 (tp30) REVERT: C 31 GLU cc_start: 0.8136 (tt0) cc_final: 0.7885 (tt0) REVERT: C 220 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.6971 (mtm180) REVERT: C 274 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7166 (tpt) REVERT: D 105 GLU cc_start: 0.7625 (tp30) cc_final: 0.7386 (tp30) REVERT: E 32 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8138 (mtmm) REVERT: E 77 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: E 106 GLU cc_start: 0.7999 (mp0) cc_final: 0.7589 (mp0) REVERT: F 43 ASN cc_start: 0.8444 (m-40) cc_final: 0.8170 (m-40) REVERT: L 13 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7600 (p) REVERT: M 70 SER cc_start: 0.8551 (m) cc_final: 0.8333 (t) REVERT: M 82 MET cc_start: 0.8679 (mtp) cc_final: 0.8465 (mtp) REVERT: N 103 HIS cc_start: 0.8286 (t-90) cc_final: 0.7906 (t-90) outliers start: 79 outliers final: 54 residues processed: 432 average time/residue: 0.6114 time to fit residues: 287.9424 Evaluate side-chains 452 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 391 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 194 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 60 optimal weight: 0.0870 chunk 117 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 111 GLN A 129 ASN A 269 ASN B 125 GLN B 154 ASN D 43 ASN E 111 GLN E 226 GLN E 295 GLN F 125 GLN F 154 ASN H 76 ASN I 76 ASN M 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105451 restraints weight = 23779.938| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.65 r_work: 0.3222 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17219 Z= 0.138 Angle : 0.542 10.249 23377 Z= 0.281 Chirality : 0.043 0.244 2523 Planarity : 0.005 0.127 3044 Dihedral : 4.840 59.391 2347 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.15 % Favored : 97.67 % Rotamer: Outliers : 3.93 % Allowed : 20.21 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2143 helix: 2.27 (0.27), residues: 372 sheet: 1.23 (0.23), residues: 457 loop : -0.55 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 81A TYR 0.014 0.001 TYR A 161 PHE 0.011 0.001 PHE F 138 TRP 0.008 0.001 TRP N 35 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00332 (17201) covalent geometry : angle 0.54040 (23341) SS BOND : bond 0.00486 ( 18) SS BOND : angle 1.30579 ( 36) hydrogen bonds : bond 0.04177 ( 681) hydrogen bonds : angle 4.87969 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 404 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7133 (pt0) cc_final: 0.6780 (mt-10) REVERT: B 27 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: B 103 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 105 GLU cc_start: 0.7806 (tp30) cc_final: 0.7488 (tp30) REVERT: C 31 GLU cc_start: 0.8108 (tt0) cc_final: 0.7870 (tt0) REVERT: C 106 GLU cc_start: 0.7915 (mp0) cc_final: 0.7697 (mp0) REVERT: C 220 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7026 (mtm180) REVERT: C 274 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7253 (tpt) REVERT: D 105 GLU cc_start: 0.7566 (tp30) cc_final: 0.7309 (tp30) REVERT: E 32 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8119 (mtmm) REVERT: E 77 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.6087 (pm20) REVERT: E 106 GLU cc_start: 0.7985 (mp0) cc_final: 0.7664 (mp0) REVERT: F 43 ASN cc_start: 0.8445 (m-40) cc_final: 0.8171 (m-40) REVERT: L 13 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7596 (p) REVERT: L 70 LYS cc_start: 0.8771 (mttp) cc_final: 0.8465 (mttm) REVERT: M 70 SER cc_start: 0.8567 (m) cc_final: 0.8315 (p) REVERT: M 82 MET cc_start: 0.8726 (mtp) cc_final: 0.8524 (mtp) REVERT: N 103 HIS cc_start: 0.8280 (t-90) cc_final: 0.7890 (t-90) outliers start: 72 outliers final: 44 residues processed: 442 average time/residue: 0.6776 time to fit residues: 327.7833 Evaluate side-chains 454 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 404 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 85 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 269 ASN B 125 GLN B 154 ASN D 43 ASN E 111 GLN E 226 GLN E 295 GLN F 125 GLN H 76 ASN I 35 ASN I 76 ASN M 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098105 restraints weight = 23717.937| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.64 r_work: 0.3203 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 17219 Z= 0.249 Angle : 0.613 12.509 23377 Z= 0.315 Chirality : 0.046 0.306 2523 Planarity : 0.005 0.128 3044 Dihedral : 5.056 58.122 2347 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.71 % Favored : 97.11 % Rotamer: Outliers : 3.93 % Allowed : 20.26 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2143 helix: 1.97 (0.27), residues: 378 sheet: 1.15 (0.23), residues: 460 loop : -0.57 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 71 TYR 0.014 0.002 TYR A 161 PHE 0.013 0.002 PHE B 110 TRP 0.010 0.001 TRP L 35 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00605 (17201) covalent geometry : angle 0.60914 (23341) SS BOND : bond 0.00714 ( 18) SS BOND : angle 1.82804 ( 36) hydrogen bonds : bond 0.04715 ( 681) hydrogen bonds : angle 4.99479 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 386 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7207 (pt0) cc_final: 0.6855 (mt-10) REVERT: A 106 GLU cc_start: 0.8175 (mp0) cc_final: 0.7922 (mp0) REVERT: A 161 TYR cc_start: 0.8911 (t80) cc_final: 0.8683 (t80) REVERT: B 27 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: B 103 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: B 105 GLU cc_start: 0.7817 (tp30) cc_final: 0.7572 (tp30) REVERT: B 143 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8324 (mmtm) REVERT: C 31 GLU cc_start: 0.8138 (tt0) cc_final: 0.7889 (tt0) REVERT: C 106 GLU cc_start: 0.7933 (mp0) cc_final: 0.7709 (mp0) REVERT: C 220 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7079 (mtm180) REVERT: E 32 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8147 (mtmm) REVERT: E 77 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.6043 (pm20) REVERT: E 106 GLU cc_start: 0.7995 (mp0) cc_final: 0.7543 (mp0) REVERT: E 295 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: L 70 LYS cc_start: 0.8784 (mttp) cc_final: 0.8478 (mttm) REVERT: M 70 SER cc_start: 0.8597 (m) cc_final: 0.8344 (p) REVERT: N 103 HIS cc_start: 0.8278 (t-90) cc_final: 0.7870 (t-90) outliers start: 72 outliers final: 45 residues processed: 430 average time/residue: 0.7143 time to fit residues: 335.2885 Evaluate side-chains 432 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 382 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 92 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 82 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 177 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 111 GLN A 129 ASN A 269 ASN B 125 GLN B 154 ASN E 226 GLN E 295 GLN F 43 ASN F 125 GLN H 76 ASN I 76 ASN M 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098802 restraints weight = 23773.282| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.65 r_work: 0.3210 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17219 Z= 0.178 Angle : 0.580 12.045 23377 Z= 0.300 Chirality : 0.044 0.279 2523 Planarity : 0.005 0.128 3044 Dihedral : 4.979 56.781 2347 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.24 % Favored : 97.62 % Rotamer: Outliers : 3.71 % Allowed : 20.64 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2143 helix: 2.13 (0.27), residues: 372 sheet: 1.17 (0.23), residues: 460 loop : -0.58 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 71 TYR 0.014 0.002 TYR A 161 PHE 0.011 0.001 PHE F 9 TRP 0.009 0.001 TRP L 35 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00431 (17201) covalent geometry : angle 0.57657 (23341) SS BOND : bond 0.00597 ( 18) SS BOND : angle 1.67694 ( 36) hydrogen bonds : bond 0.04403 ( 681) hydrogen bonds : angle 4.91530 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 394 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7155 (pt0) cc_final: 0.6811 (mt-10) REVERT: A 106 GLU cc_start: 0.8169 (mp0) cc_final: 0.7921 (mp0) REVERT: A 187 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7887 (p0) REVERT: B 27 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: B 103 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 105 GLU cc_start: 0.7812 (tp30) cc_final: 0.7557 (tp30) REVERT: B 143 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8321 (mmtm) REVERT: C 31 GLU cc_start: 0.8090 (tt0) cc_final: 0.7838 (tt0) REVERT: C 106 GLU cc_start: 0.7926 (mp0) cc_final: 0.7703 (mp0) REVERT: C 220 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7058 (mtm180) REVERT: C 274 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7270 (tpt) REVERT: E 32 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8127 (mtmm) REVERT: E 77 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: E 106 GLU cc_start: 0.8002 (mp0) cc_final: 0.7614 (mp0) REVERT: F 43 ASN cc_start: 0.8476 (m-40) cc_final: 0.8221 (m-40) REVERT: M 70 SER cc_start: 0.8602 (m) cc_final: 0.8349 (p) REVERT: N 103 HIS cc_start: 0.8286 (t-90) cc_final: 0.7877 (t-90) outliers start: 68 outliers final: 50 residues processed: 432 average time/residue: 0.6885 time to fit residues: 325.0514 Evaluate side-chains 446 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 390 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 92 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 168 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 111 GLN A 129 ASN A 269 ASN B 125 GLN B 154 ASN D 38 GLN E 226 GLN E 295 GLN F 125 GLN F 154 ASN H 76 ASN I 35 ASN I 76 ASN M 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098751 restraints weight = 23819.594| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.65 r_work: 0.3215 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17219 Z= 0.181 Angle : 0.578 11.436 23377 Z= 0.298 Chirality : 0.044 0.269 2523 Planarity : 0.005 0.128 3044 Dihedral : 4.965 54.923 2347 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.38 % Favored : 97.48 % Rotamer: Outliers : 3.71 % Allowed : 20.64 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2143 helix: 2.09 (0.27), residues: 372 sheet: 1.16 (0.23), residues: 460 loop : -0.57 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 71 TYR 0.018 0.002 TYR A 161 PHE 0.011 0.001 PHE F 9 TRP 0.009 0.001 TRP L 35 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00439 (17201) covalent geometry : angle 0.57469 (23341) SS BOND : bond 0.00564 ( 18) SS BOND : angle 1.63107 ( 36) hydrogen bonds : bond 0.04396 ( 681) hydrogen bonds : angle 4.88793 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 391 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7168 (pt0) cc_final: 0.6842 (mt-10) REVERT: A 106 GLU cc_start: 0.8185 (mp0) cc_final: 0.7936 (mp0) REVERT: A 187 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7880 (p0) REVERT: B 27 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: B 103 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: B 143 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8303 (mmtm) REVERT: C 106 GLU cc_start: 0.7930 (mp0) cc_final: 0.7722 (mp0) REVERT: C 220 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7052 (mtm180) REVERT: C 274 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7260 (tpt) REVERT: E 77 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.6024 (pm20) REVERT: E 106 GLU cc_start: 0.7990 (mp0) cc_final: 0.7667 (mp0) REVERT: L 13 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7640 (p) REVERT: M 70 SER cc_start: 0.8610 (m) cc_final: 0.8355 (p) REVERT: N 103 HIS cc_start: 0.8292 (t-90) cc_final: 0.7881 (t-90) outliers start: 68 outliers final: 52 residues processed: 429 average time/residue: 0.6259 time to fit residues: 293.3969 Evaluate side-chains 449 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 92 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 197 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 76 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 111 GLN A 129 ASN A 269 ASN B 125 GLN B 154 ASN C 111 GLN E 226 GLN E 295 GLN F 43 ASN F 125 GLN H 76 ASN I 35 ASN I 76 ASN M 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099265 restraints weight = 23753.106| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.65 r_work: 0.3225 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17219 Z= 0.150 Angle : 0.583 14.973 23377 Z= 0.299 Chirality : 0.044 0.338 2523 Planarity : 0.005 0.128 3044 Dihedral : 4.889 56.409 2347 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 3.28 % Allowed : 21.14 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2143 helix: 2.15 (0.27), residues: 372 sheet: 1.18 (0.23), residues: 460 loop : -0.55 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 71 TYR 0.015 0.001 TYR A 161 PHE 0.010 0.001 PHE F 9 TRP 0.008 0.001 TRP N 35 HIS 0.004 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00363 (17201) covalent geometry : angle 0.57716 (23341) SS BOND : bond 0.00616 ( 18) SS BOND : angle 2.13460 ( 36) hydrogen bonds : bond 0.04181 ( 681) hydrogen bonds : angle 4.83644 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 399 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7150 (pt0) cc_final: 0.6805 (mt-10) REVERT: A 106 GLU cc_start: 0.8179 (mp0) cc_final: 0.7962 (mp0) REVERT: A 187 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 27 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: B 103 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 105 GLU cc_start: 0.7791 (tp30) cc_final: 0.7535 (tp30) REVERT: B 143 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8288 (mmtm) REVERT: C 106 GLU cc_start: 0.7915 (mp0) cc_final: 0.7707 (mp0) REVERT: C 220 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7062 (mtm180) REVERT: C 274 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7261 (tpt) REVERT: C 280 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8249 (ttpp) REVERT: E 32 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8108 (mtmm) REVERT: E 106 GLU cc_start: 0.7972 (mp0) cc_final: 0.7541 (mp0) REVERT: F 43 ASN cc_start: 0.8461 (m-40) cc_final: 0.8207 (m-40) REVERT: H 82 MET cc_start: 0.8486 (mtp) cc_final: 0.8067 (ptp) REVERT: L 13 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7645 (p) REVERT: M 70 SER cc_start: 0.8613 (m) cc_final: 0.8347 (p) REVERT: M 76 ASN cc_start: 0.8445 (m-40) cc_final: 0.8236 (m-40) REVERT: N 103 HIS cc_start: 0.8298 (t-90) cc_final: 0.7886 (t-90) outliers start: 60 outliers final: 48 residues processed: 431 average time/residue: 0.6127 time to fit residues: 289.2878 Evaluate side-chains 448 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 394 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 92 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 183 optimal weight: 0.4980 chunk 194 optimal weight: 0.9990 chunk 205 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 111 GLN A 129 ASN A 269 ASN B 125 GLN B 154 ASN C 111 GLN C 226 GLN E 226 GLN E 295 GLN F 125 GLN H 76 ASN I 35 ASN I 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098345 restraints weight = 23709.186| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.65 r_work: 0.3223 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17219 Z= 0.174 Angle : 0.595 14.244 23377 Z= 0.305 Chirality : 0.045 0.318 2523 Planarity : 0.005 0.128 3044 Dihedral : 4.920 58.210 2347 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.47 % Favored : 97.39 % Rotamer: Outliers : 3.50 % Allowed : 21.35 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2143 helix: 2.10 (0.27), residues: 372 sheet: 1.16 (0.23), residues: 460 loop : -0.56 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 71 TYR 0.017 0.001 TYR A 161 PHE 0.011 0.001 PHE F 9 TRP 0.008 0.001 TRP L 35 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00422 (17201) covalent geometry : angle 0.58841 (23341) SS BOND : bond 0.00618 ( 18) SS BOND : angle 2.24985 ( 36) hydrogen bonds : bond 0.04299 ( 681) hydrogen bonds : angle 4.84312 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7212.40 seconds wall clock time: 123 minutes 19.52 seconds (7399.52 seconds total)