Starting phenix.real_space_refine on Wed Mar 4 22:26:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oi3_70503/03_2026/9oi3_70503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oi3_70503/03_2026/9oi3_70503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oi3_70503/03_2026/9oi3_70503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oi3_70503/03_2026/9oi3_70503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oi3_70503/03_2026/9oi3_70503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oi3_70503/03_2026/9oi3_70503.map" } resolution = 2.71 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= 0.020 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 80 5.16 5 C 10394 2.51 5 N 2859 2.21 5 O 3152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16485 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2428 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1334 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2386 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 20, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 12, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1330 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1338 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 977 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "I" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 796 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "M" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 121} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 790 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.19, per 1000 atoms: 0.25 Number of scatterers: 16485 At special positions: 0 Unit cell: (121.67, 133.308, 150.236, 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 80 16.00 O 3152 8.00 N 2859 7.00 C 10394 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=2.03 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=2.03 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=2.02 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=2.03 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=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.08 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: 1.48 Conformation dependent library (CDL) restraints added in 851.8 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 51 sheets defined 19.9% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.886A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.422A pdb=" N SER A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.922A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.167A 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 76 through 80 removed outlier: 3.764A pdb=" N ILE C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 196 removed outlier: 3.668A pdb=" N LEU C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 126 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 169 removed outlier: 3.557A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.877A pdb=" N LEU E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 80 " --> pdb=" O GLU E 77 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.671A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 170 removed outlier: 3.901A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.914A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.957A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.075A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.575A pdb=" N ARG M 64 " --> pdb=" O SER M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 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 25 through 26 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 54 removed outlier: 5.791A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.396A 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: 6.710A 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 117 removed outlier: 6.381A pdb=" N SER A 261 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.638A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AB2, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.752A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 14 removed outlier: 8.437A pdb=" N TRP D 14 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR C 17 " --> pdb=" O TRP D 14 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 13 through 14 removed outlier: 8.437A pdb=" N TRP D 14 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR C 17 " --> pdb=" O TRP D 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.216A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'C' and resid 51 through 54 removed outlier: 7.586A pdb=" N LEU C 51 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA C 279 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU C 53 " --> pdb=" O ALA C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.351A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.659A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC5, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.540A pdb=" N PHE F 138 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.125A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD2, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD3, first strand: chain 'E' and resid 59 through 61 Processing sheet with id=AD4, first strand: chain 'E' and resid 115 through 121 removed outlier: 6.425A pdb=" N SER E 261 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE E 118 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (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 151 through 153 Processing sheet with id=AD7, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD8, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.514A pdb=" N ILE E 288 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.646A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.909A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.428A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.428A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.701A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.370A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.522A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'N' and resid 4 through 6 removed outlier: 12.273A pdb=" N CYS N 23 " --> pdb=" O THR N 74 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N THR N 74 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N ALA N 25 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N THR N 72 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N GLN N 27 " --> pdb=" O GLU N 70 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU N 70 " --> pdb=" O GLN N 27 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.596A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3447 1.33 - 1.46: 5443 1.46 - 1.59: 7875 1.59 - 1.72: 0 1.72 - 1.85: 112 Bond restraints: 16877 Sorted by residual: bond pdb=" C SER E 210 " pdb=" N ARG E 211 " ideal model delta sigma weight residual 1.331 1.259 0.072 1.25e-02 6.40e+03 3.35e+01 bond pdb=" C ASN C 171 " pdb=" N LYS C 172 " ideal model delta sigma weight residual 1.331 1.410 -0.079 1.43e-02 4.89e+03 3.05e+01 bond pdb=" CA THR M 107 " pdb=" C THR M 107 " ideal model delta sigma weight residual 1.533 1.487 0.046 9.60e-03 1.09e+04 2.34e+01 bond pdb=" C LYS A 222 " pdb=" N VAL A 223 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" C ARG E 211 " pdb=" N LYS E 212 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.44e-02 4.82e+03 2.19e+01 ... (remaining 16872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 22120 2.58 - 5.16: 731 5.16 - 7.73: 75 7.73 - 10.31: 13 10.31 - 12.89: 2 Bond angle restraints: 22941 Sorted by residual: angle pdb=" N LYS E 280 " pdb=" CA LYS E 280 " pdb=" C LYS E 280 " ideal model delta sigma weight residual 114.12 104.85 9.27 1.39e+00 5.18e-01 4.45e+01 angle pdb=" C PHE F 9 " pdb=" CA PHE F 9 " pdb=" CB PHE F 9 " ideal model delta sigma weight residual 110.42 123.31 -12.89 1.99e+00 2.53e-01 4.20e+01 angle pdb=" CA PHE D 9 " pdb=" CB PHE D 9 " pdb=" CG PHE D 9 " ideal model delta sigma weight residual 113.80 120.27 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" C PHE D 9 " pdb=" CA PHE D 9 " pdb=" CB PHE D 9 " ideal model delta sigma weight residual 110.42 122.72 -12.30 1.99e+00 2.53e-01 3.82e+01 angle pdb=" CA PHE F 9 " pdb=" CB PHE F 9 " pdb=" CG PHE F 9 " ideal model delta sigma weight residual 113.80 118.88 -5.08 1.00e+00 1.00e+00 2.58e+01 ... (remaining 22936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8488 17.98 - 35.95: 1073 35.95 - 53.93: 328 53.93 - 71.90: 55 71.90 - 89.88: 17 Dihedral angle restraints: 9961 sinusoidal: 3757 harmonic: 6204 Sorted by residual: dihedral pdb=" CD ARG A 82 " pdb=" NE ARG A 82 " pdb=" CZ ARG A 82 " pdb=" NH1 ARG A 82 " ideal model delta sinusoidal sigma weight residual 0.00 -85.21 85.21 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CD ARG E 82 " pdb=" NE ARG E 82 " pdb=" CZ ARG E 82 " pdb=" NH1 ARG E 82 " ideal model delta sinusoidal sigma weight residual 0.00 -77.09 77.09 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CD ARG I 66 " pdb=" NE ARG I 66 " pdb=" CZ ARG I 66 " pdb=" NH1 ARG I 66 " ideal model delta sinusoidal sigma weight residual 0.00 -69.61 69.61 1 1.00e+01 1.00e-02 6.25e+01 ... (remaining 9958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2065 0.067 - 0.133: 368 0.133 - 0.200: 63 0.200 - 0.267: 15 0.267 - 0.333: 5 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA LYS C 197 " pdb=" N LYS C 197 " pdb=" C LYS C 197 " pdb=" CB LYS C 197 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA GLU C 119 " pdb=" N GLU C 119 " pdb=" C GLU C 119 " pdb=" CB GLU C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA VAL B 18 " pdb=" N VAL B 18 " pdb=" C VAL B 18 " pdb=" CB VAL B 18 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2513 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 82 " 1.110 9.50e-02 1.11e+02 4.98e-01 1.49e+02 pdb=" NE ARG E 82 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG E 82 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 82 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 82 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 82 " -1.095 9.50e-02 1.11e+02 4.91e-01 1.45e+02 pdb=" NE ARG A 82 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 82 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 82 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 82 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 66 " 1.028 9.50e-02 1.11e+02 4.61e-01 1.28e+02 pdb=" NE ARG I 66 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG I 66 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG I 66 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG I 66 " 0.022 2.00e-02 2.50e+03 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 176 2.62 - 3.19: 13532 3.19 - 3.76: 25280 3.76 - 4.33: 35794 4.33 - 4.90: 60480 Nonbonded interactions: 135262 Sorted by model distance: nonbonded pdb=" O ASN D 60 " pdb=" OD1 ASN D 60 " model vdw 2.052 3.040 nonbonded pdb=" NH2 ARG C 82 " pdb=" O SER C 83A" model vdw 2.201 3.120 nonbonded pdb=" OH TYR F 119 " pdb=" OE2 GLU F 132 " model vdw 2.207 3.040 nonbonded pdb=" O SER L 31 " pdb=" OG SER L 31 " model vdw 2.209 3.040 nonbonded pdb=" O PRO C 58 " pdb=" NH1 ARG C 82 " model vdw 2.220 3.120 ... (remaining 135257 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 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 141 or (resid 142 and (name N or n \ ame CA or name C or name O or name CB )) or resid 143 through 159 or (resid 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 17 \ 3 or (resid 174 through 175 and (name N or name CA or name C or name O or name C \ B )) or resid 176 through 186 or (resid 187 through 188 and (name N or name CA o \ r name C or name O or name CB )) or resid 189 through 224 or (resid 225 through \ 227 and (name N or name CA or name C or name O or name CB )) or resid 228 throug \ h 262A or resid 265 through 273 or (resid 274 through 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 324)) selection = (chain 'C' and (resid 11 through 273 or (resid 274 through 276 and (name N or na \ me CA or name C or name O or name CB )) or resid 277 through 324)) selection = (chain 'E' and (resid 11 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 116 or (resid 117 and (name N or n \ ame CA or name C or name O or name CB )) or resid 118 through 187 or (resid 188 \ and (name N or name CA or name C or name O or name CB )) or resid 189 through 27 \ 5 or (resid 276 and (name N or name CA or name C or name O or name CB )) or resi \ d 277 through 324)) } ncs_group { reference = (chain 'B' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 142 or (resid 143 and \ (name N or name CA or name C or name O or name CB )) or resid 144 through 170)) selection = (chain 'D' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 170)) selection = (chain 'F' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 61 or (resid 62 and (n \ ame N or name CA or name C or name O or name CB )) or resid 63 through 142 or (r \ esid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 t \ hrough 170)) } ncs_group { reference = (chain 'H' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 104 or (resid 105 and (name N or name \ CA or name C or name O or name CB )) or resid 106 through 110)) selection = (chain 'I' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 104 or (resid 105 and (name N or name \ CA or name C or name O or name CB )) or resid 106 through 110)) selection = (chain 'M' and resid 2 through 110) } ncs_group { reference = (chain 'J' and (resid 2 through 82 or (resid 83 through 84 and (name N or name C \ A or name C or name O or name CB )) or resid 85 through 104)) selection = (chain 'L' and (resid 2 through 82 or (resid 83 through 84 and (name N or name C \ A or name C or name O or name CB )) or resid 85 through 104)) selection = (chain 'N' and resid 2 through 104) } 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: 3.750 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.370 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 16895 Z= 0.417 Angle : 0.983 12.890 22977 Z= 0.633 Chirality : 0.056 0.333 2516 Planarity : 0.023 0.498 2955 Dihedral : 17.600 89.877 5953 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.79 % Favored : 94.02 % Rotamer: Outliers : 3.76 % Allowed : 27.78 % Favored : 68.45 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2124 helix: 1.86 (0.27), residues: 361 sheet: 0.64 (0.24), residues: 513 loop : -1.42 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 82 TYR 0.023 0.002 TYR M 100J PHE 0.016 0.002 PHE E 121 TRP 0.022 0.002 TRP H 103 HIS 0.010 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00658 (16877) covalent geometry : angle 0.98085 (22941) SS BOND : bond 0.01330 ( 18) SS BOND : angle 1.93468 ( 36) hydrogen bonds : bond 0.15282 ( 659) hydrogen bonds : angle 6.44865 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 407 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 229 ARG cc_start: 0.8484 (mmt-90) cc_final: 0.7975 (mpt180) REVERT: A 282 GLN cc_start: 0.8059 (tp40) cc_final: 0.7827 (mm-40) REVERT: A 301 THR cc_start: 0.8244 (p) cc_final: 0.7967 (p) REVERT: B 97 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7343 (mp0) REVERT: C 106 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: C 118 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8017 (t80) REVERT: C 119 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: C 172 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8341 (mtpt) REVERT: C 191 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: C 274 MET cc_start: 0.6831 (tmm) cc_final: 0.6543 (tmm) REVERT: C 320 LEU cc_start: 0.8215 (mp) cc_final: 0.7940 (mt) REVERT: D 69 GLU cc_start: 0.7615 (pm20) cc_final: 0.7397 (pm20) REVERT: E 203 SER cc_start: 0.8678 (m) cc_final: 0.8376 (t) REVERT: E 301 THR cc_start: 0.8294 (p) cc_final: 0.7872 (t) REVERT: H 100 PHE cc_start: 0.8627 (m-10) cc_final: 0.8423 (m-10) REVERT: H 110 THR cc_start: 0.8436 (p) cc_final: 0.8094 (t) REVERT: I 20 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8452 (mt) REVERT: I 68 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8524 (m) REVERT: I 69 MET cc_start: 0.8772 (mtp) cc_final: 0.8531 (mtp) REVERT: J 69 THR cc_start: 0.8450 (p) cc_final: 0.8081 (m) REVERT: L 3 GLN cc_start: 0.7744 (mp10) cc_final: 0.7507 (mp10) REVERT: L 79 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6811 (mp10) REVERT: N 5 THR cc_start: 0.8226 (m) cc_final: 0.7883 (p) REVERT: N 37 GLN cc_start: 0.8566 (tt0) cc_final: 0.8008 (pt0) REVERT: N 69 THR cc_start: 0.8717 (p) cc_final: 0.8263 (m) REVERT: N 74 THR cc_start: 0.8135 (m) cc_final: 0.7908 (p) outliers start: 66 outliers final: 30 residues processed: 439 average time/residue: 0.6676 time to fit residues: 321.2288 Evaluate side-chains 438 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 401 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 22 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0370 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 196 HIS A 269 ASN C 101 HIS C 269 ASN C 322 ASN D 43 ASN D 60 ASN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN F 125 GLN L 90 GLN N 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.115401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105584 restraints weight = 24401.946| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.76 r_work: 0.3343 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16895 Z= 0.143 Angle : 0.570 9.101 22977 Z= 0.298 Chirality : 0.042 0.129 2516 Planarity : 0.004 0.047 2955 Dihedral : 6.727 77.938 2397 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.05 % Allowed : 26.30 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2124 helix: 2.47 (0.27), residues: 363 sheet: 0.79 (0.24), residues: 517 loop : -1.21 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 220 TYR 0.012 0.001 TYR I 50 PHE 0.010 0.001 PHE B 9 TRP 0.013 0.001 TRP F 21 HIS 0.005 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00326 (16877) covalent geometry : angle 0.56962 (22941) SS BOND : bond 0.00413 ( 18) SS BOND : angle 0.96874 ( 36) hydrogen bonds : bond 0.04520 ( 659) hydrogen bonds : angle 4.88772 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 389 time to evaluate : 0.589 Fit side-chains REVERT: A 229 ARG cc_start: 0.8530 (mmt-90) cc_final: 0.8174 (mpt180) REVERT: B 22 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: B 97 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7308 (mp0) REVERT: C 106 GLU cc_start: 0.7725 (mp0) cc_final: 0.7435 (mp0) REVERT: C 274 MET cc_start: 0.6763 (tmm) cc_final: 0.6436 (tmm) REVERT: D 68 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8241 (mttm) REVERT: D 101 LEU cc_start: 0.8027 (mp) cc_final: 0.7746 (mt) REVERT: E 75 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5839 (mt-10) REVERT: E 203 SER cc_start: 0.8660 (m) cc_final: 0.8375 (p) REVERT: E 281 CYS cc_start: 0.7008 (t) cc_final: 0.6620 (t) REVERT: H 100 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8083 (mtm-85) REVERT: I 4 LEU cc_start: 0.8745 (mt) cc_final: 0.8497 (mp) REVERT: I 68 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8547 (m) REVERT: I 69 MET cc_start: 0.8656 (mtp) cc_final: 0.8390 (mtp) REVERT: J 69 THR cc_start: 0.8437 (p) cc_final: 0.8075 (m) REVERT: L 3 GLN cc_start: 0.7737 (mp10) cc_final: 0.7450 (mp10) REVERT: L 79 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: N 5 THR cc_start: 0.8210 (m) cc_final: 0.7869 (p) REVERT: N 22 THR cc_start: 0.8402 (m) cc_final: 0.8042 (p) REVERT: N 69 THR cc_start: 0.8663 (p) cc_final: 0.8294 (m) REVERT: N 74 THR cc_start: 0.8109 (m) cc_final: 0.7880 (p) outliers start: 71 outliers final: 29 residues processed: 424 average time/residue: 0.6667 time to fit residues: 310.3640 Evaluate side-chains 398 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 364 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 99 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 118 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 322 ASN D 43 ASN D 125 GLN F 125 GLN F 135 ASN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103604 restraints weight = 24448.923| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.76 r_work: 0.3312 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16895 Z= 0.240 Angle : 0.608 9.885 22977 Z= 0.314 Chirality : 0.044 0.134 2516 Planarity : 0.004 0.051 2955 Dihedral : 5.497 75.093 2347 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.22 % Allowed : 25.27 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2124 helix: 2.45 (0.26), residues: 363 sheet: 0.71 (0.24), residues: 519 loop : -1.14 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.015 0.002 TYR I 50 PHE 0.013 0.002 PHE A 121 TRP 0.015 0.001 TRP F 21 HIS 0.007 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00563 (16877) covalent geometry : angle 0.60597 (22941) SS BOND : bond 0.00437 ( 18) SS BOND : angle 1.25602 ( 36) hydrogen bonds : bond 0.04805 ( 659) hydrogen bonds : angle 4.85184 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 383 time to evaluate : 0.612 Fit side-chains REVERT: B 22 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: B 97 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7364 (mp0) REVERT: B 135 ASN cc_start: 0.7377 (t0) cc_final: 0.6923 (t0) REVERT: B 143 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8238 (mmmm) REVERT: C 106 GLU cc_start: 0.7800 (mp0) cc_final: 0.7373 (mp0) REVERT: C 274 MET cc_start: 0.6848 (tmm) cc_final: 0.6506 (tmm) REVERT: E 203 SER cc_start: 0.8642 (m) cc_final: 0.8362 (p) REVERT: E 262 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.6752 (mmt-90) REVERT: E 281 CYS cc_start: 0.7064 (t) cc_final: 0.6669 (t) REVERT: H 5 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: I 4 LEU cc_start: 0.8756 (mt) cc_final: 0.8509 (mp) REVERT: I 69 MET cc_start: 0.8684 (mtp) cc_final: 0.8430 (mtp) REVERT: J 69 THR cc_start: 0.8448 (p) cc_final: 0.8036 (m) REVERT: L 3 GLN cc_start: 0.7791 (mp10) cc_final: 0.7470 (mp10) REVERT: L 79 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: N 5 THR cc_start: 0.8254 (m) cc_final: 0.7911 (p) REVERT: N 69 THR cc_start: 0.8661 (p) cc_final: 0.8275 (m) REVERT: N 74 THR cc_start: 0.8110 (m) cc_final: 0.7903 (p) outliers start: 74 outliers final: 42 residues processed: 414 average time/residue: 0.6087 time to fit residues: 278.4144 Evaluate side-chains 414 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 369 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 271 ASN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 123 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 92 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 96 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 125 GLN C 282 GLN D 43 ASN D 125 GLN F 125 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105699 restraints weight = 24402.236| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.74 r_work: 0.3348 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16895 Z= 0.112 Angle : 0.521 8.948 22977 Z= 0.271 Chirality : 0.041 0.133 2516 Planarity : 0.004 0.046 2955 Dihedral : 5.032 71.620 2344 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.94 % Allowed : 26.47 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2124 helix: 2.90 (0.27), residues: 363 sheet: 0.88 (0.24), residues: 520 loop : -1.10 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 38 TYR 0.010 0.001 TYR E 195 PHE 0.008 0.001 PHE C 213 TRP 0.011 0.001 TRP F 21 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00256 (16877) covalent geometry : angle 0.52027 (22941) SS BOND : bond 0.00291 ( 18) SS BOND : angle 0.90329 ( 36) hydrogen bonds : bond 0.03993 ( 659) hydrogen bonds : angle 4.58514 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 377 time to evaluate : 0.603 Fit side-chains REVERT: A 131 THR cc_start: 0.8646 (m) cc_final: 0.8283 (p) REVERT: B 22 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: B 97 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7328 (mp0) REVERT: B 135 ASN cc_start: 0.7248 (t0) cc_final: 0.7045 (t0) REVERT: B 143 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8199 (mmmm) REVERT: C 106 GLU cc_start: 0.7733 (mp0) cc_final: 0.7321 (mp0) REVERT: C 274 MET cc_start: 0.6827 (tmm) cc_final: 0.6445 (tmm) REVERT: E 203 SER cc_start: 0.8622 (m) cc_final: 0.8349 (p) REVERT: E 281 CYS cc_start: 0.7105 (t) cc_final: 0.6700 (t) REVERT: H 5 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: H 79 SER cc_start: 0.8210 (t) cc_final: 0.7991 (m) REVERT: H 100 PHE cc_start: 0.8679 (m-10) cc_final: 0.8454 (m-10) REVERT: I 11 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8430 (tp) REVERT: I 69 MET cc_start: 0.8644 (mtp) cc_final: 0.8417 (mtp) REVERT: J 69 THR cc_start: 0.8430 (p) cc_final: 0.8033 (m) REVERT: L 3 GLN cc_start: 0.7751 (mp10) cc_final: 0.7418 (mp10) REVERT: L 79 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7266 (mp10) REVERT: N 5 THR cc_start: 0.8140 (m) cc_final: 0.7829 (p) REVERT: N 74 THR cc_start: 0.8067 (m) cc_final: 0.7849 (p) outliers start: 69 outliers final: 31 residues processed: 416 average time/residue: 0.6064 time to fit residues: 278.8361 Evaluate side-chains 403 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 368 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 125 GLN D 43 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 135 ASN L 37 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103870 restraints weight = 24379.634| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.77 r_work: 0.3318 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16895 Z= 0.200 Angle : 0.575 9.824 22977 Z= 0.296 Chirality : 0.043 0.230 2516 Planarity : 0.004 0.049 2955 Dihedral : 5.011 73.108 2340 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.05 % Allowed : 26.47 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2124 helix: 2.75 (0.27), residues: 363 sheet: 0.83 (0.24), residues: 512 loop : -1.07 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 310 TYR 0.016 0.002 TYR I 50 PHE 0.011 0.002 PHE F 9 TRP 0.014 0.001 TRP F 21 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00471 (16877) covalent geometry : angle 0.57137 (22941) SS BOND : bond 0.00552 ( 18) SS BOND : angle 1.66732 ( 36) hydrogen bonds : bond 0.04444 ( 659) hydrogen bonds : angle 4.66595 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 385 time to evaluate : 0.494 Fit side-chains REVERT: A 131 THR cc_start: 0.8645 (m) cc_final: 0.8263 (p) REVERT: B 22 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: B 97 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7390 (mp0) REVERT: B 135 ASN cc_start: 0.7444 (t0) cc_final: 0.7165 (t0) REVERT: C 106 GLU cc_start: 0.7753 (mp0) cc_final: 0.7268 (mp0) REVERT: C 274 MET cc_start: 0.6860 (tmm) cc_final: 0.6475 (tmm) REVERT: D 59 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8054 (ttp) REVERT: D 101 LEU cc_start: 0.8105 (mp) cc_final: 0.7827 (mt) REVERT: E 203 SER cc_start: 0.8641 (m) cc_final: 0.8353 (p) REVERT: E 281 CYS cc_start: 0.7096 (t) cc_final: 0.6687 (t) REVERT: H 5 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: H 79 SER cc_start: 0.8275 (t) cc_final: 0.8047 (m) REVERT: H 87 THR cc_start: 0.8873 (p) cc_final: 0.8638 (t) REVERT: H 110 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7900 (t) REVERT: I 4 LEU cc_start: 0.8752 (mt) cc_final: 0.8488 (mp) REVERT: I 69 MET cc_start: 0.8659 (mtp) cc_final: 0.8437 (mtp) REVERT: J 69 THR cc_start: 0.8450 (p) cc_final: 0.8024 (m) REVERT: L 3 GLN cc_start: 0.7802 (mp10) cc_final: 0.7488 (mp10) REVERT: L 100 GLN cc_start: 0.7934 (mp10) cc_final: 0.7377 (mp10) REVERT: N 5 THR cc_start: 0.8279 (m) cc_final: 0.7951 (p) REVERT: N 74 THR cc_start: 0.8013 (m) cc_final: 0.7812 (p) REVERT: N 77 SER cc_start: 0.7639 (p) cc_final: 0.7415 (p) outliers start: 71 outliers final: 39 residues processed: 418 average time/residue: 0.6123 time to fit residues: 282.6291 Evaluate side-chains 416 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 373 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 204 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 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 269 ASN B 125 GLN D 43 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN F 125 GLN N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104165 restraints weight = 24300.547| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.76 r_work: 0.3323 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16895 Z= 0.175 Angle : 0.564 10.541 22977 Z= 0.290 Chirality : 0.042 0.241 2516 Planarity : 0.004 0.047 2955 Dihedral : 4.972 75.432 2340 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.99 % Allowed : 26.70 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2124 helix: 2.76 (0.26), residues: 363 sheet: 0.92 (0.24), residues: 507 loop : -1.10 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 310 TYR 0.013 0.002 TYR I 50 PHE 0.011 0.001 PHE C 245 TRP 0.012 0.001 TRP F 21 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00412 (16877) covalent geometry : angle 0.55999 (22941) SS BOND : bond 0.00513 ( 18) SS BOND : angle 1.73146 ( 36) hydrogen bonds : bond 0.04311 ( 659) hydrogen bonds : angle 4.64351 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 382 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 131 THR cc_start: 0.8638 (m) cc_final: 0.8239 (p) REVERT: A 157 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7684 (tptm) REVERT: A 197 LYS cc_start: 0.8293 (ptpt) cc_final: 0.8075 (ptpt) REVERT: B 22 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: B 132 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: B 135 ASN cc_start: 0.7480 (t0) cc_final: 0.7217 (t0) REVERT: B 143 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8206 (mmmm) REVERT: C 106 GLU cc_start: 0.7789 (mp0) cc_final: 0.7310 (mp0) REVERT: C 274 MET cc_start: 0.6826 (tmm) cc_final: 0.6527 (tmm) REVERT: D 59 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7944 (ttp) REVERT: D 69 GLU cc_start: 0.7410 (pm20) cc_final: 0.7200 (pm20) REVERT: D 101 LEU cc_start: 0.8076 (mp) cc_final: 0.7797 (mt) REVERT: E 203 SER cc_start: 0.8638 (m) cc_final: 0.8352 (p) REVERT: E 281 CYS cc_start: 0.7091 (t) cc_final: 0.6675 (t) REVERT: H 5 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: H 79 SER cc_start: 0.8261 (t) cc_final: 0.8040 (m) REVERT: H 87 THR cc_start: 0.8866 (p) cc_final: 0.8616 (t) REVERT: H 100 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8190 (t0) REVERT: H 110 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7876 (t) REVERT: I 68 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8502 (m) REVERT: J 69 THR cc_start: 0.8432 (p) cc_final: 0.8009 (m) REVERT: L 3 GLN cc_start: 0.7796 (mp10) cc_final: 0.7466 (mp10) REVERT: L 100 GLN cc_start: 0.7939 (mp10) cc_final: 0.7395 (mp10) REVERT: N 5 THR cc_start: 0.8295 (m) cc_final: 0.7961 (p) REVERT: N 77 SER cc_start: 0.7572 (p) cc_final: 0.7354 (p) outliers start: 70 outliers final: 47 residues processed: 416 average time/residue: 0.6231 time to fit residues: 286.0614 Evaluate side-chains 439 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 384 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 15 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 157 optimal weight: 0.0040 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 125 GLN D 43 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN F 125 GLN F 135 ASN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104151 restraints weight = 24334.985| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.76 r_work: 0.3328 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16895 Z= 0.164 Angle : 0.561 12.269 22977 Z= 0.289 Chirality : 0.042 0.238 2516 Planarity : 0.004 0.047 2955 Dihedral : 4.944 77.181 2340 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.94 % Allowed : 27.55 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2124 helix: 2.78 (0.26), residues: 363 sheet: 0.90 (0.24), residues: 497 loop : -1.04 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 310 TYR 0.011 0.002 TYR I 50 PHE 0.011 0.001 PHE C 245 TRP 0.013 0.001 TRP F 21 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00387 (16877) covalent geometry : angle 0.55715 (22941) SS BOND : bond 0.00521 ( 18) SS BOND : angle 1.68576 ( 36) hydrogen bonds : bond 0.04257 ( 659) hydrogen bonds : angle 4.63223 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 385 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 131 THR cc_start: 0.8642 (m) cc_final: 0.8253 (p) REVERT: A 197 LYS cc_start: 0.8291 (ptpt) cc_final: 0.8072 (ptpt) REVERT: B 22 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: B 123 LYS cc_start: 0.8712 (tttp) cc_final: 0.8390 (tttm) REVERT: B 132 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: B 135 ASN cc_start: 0.7552 (t0) cc_final: 0.7289 (t0) REVERT: B 143 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8206 (mmmm) REVERT: C 106 GLU cc_start: 0.7810 (mp0) cc_final: 0.7319 (mp0) REVERT: C 274 MET cc_start: 0.6856 (tmm) cc_final: 0.6532 (tmm) REVERT: D 59 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7908 (ttp) REVERT: D 69 GLU cc_start: 0.7394 (pm20) cc_final: 0.7180 (pm20) REVERT: D 101 LEU cc_start: 0.8070 (mp) cc_final: 0.7794 (mt) REVERT: E 203 SER cc_start: 0.8619 (m) cc_final: 0.8355 (p) REVERT: E 211 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7317 (ttp80) REVERT: E 281 CYS cc_start: 0.7089 (t) cc_final: 0.6663 (t) REVERT: H 5 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6618 (pm20) REVERT: H 79 SER cc_start: 0.8246 (t) cc_final: 0.8030 (m) REVERT: H 87 THR cc_start: 0.8871 (p) cc_final: 0.8613 (t) REVERT: H 100 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8195 (t0) REVERT: H 110 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7869 (t) REVERT: I 4 LEU cc_start: 0.8738 (mt) cc_final: 0.8465 (mp) REVERT: I 68 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8469 (m) REVERT: J 69 THR cc_start: 0.8430 (p) cc_final: 0.7996 (m) REVERT: L 3 GLN cc_start: 0.7799 (mp10) cc_final: 0.7470 (mp10) REVERT: N 5 THR cc_start: 0.8306 (m) cc_final: 0.7958 (p) REVERT: N 77 SER cc_start: 0.7533 (p) cc_final: 0.7324 (p) outliers start: 69 outliers final: 42 residues processed: 420 average time/residue: 0.6035 time to fit residues: 280.2857 Evaluate side-chains 429 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 379 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 178 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 162 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 197 optimal weight: 0.0050 chunk 74 optimal weight: 0.0470 chunk 110 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 125 GLN D 43 ASN D 125 GLN E 170 ASN F 125 GLN F 135 ASN N 38 GLN N 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104973 restraints weight = 24387.637| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.77 r_work: 0.3338 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16895 Z= 0.131 Angle : 0.550 12.844 22977 Z= 0.282 Chirality : 0.042 0.214 2516 Planarity : 0.004 0.046 2955 Dihedral : 4.823 80.352 2339 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.76 % Allowed : 27.38 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2124 helix: 2.93 (0.27), residues: 363 sheet: 1.00 (0.24), residues: 505 loop : -1.03 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.010 0.001 TYR M 33 PHE 0.010 0.001 PHE B 9 TRP 0.012 0.001 TRP F 21 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00306 (16877) covalent geometry : angle 0.54732 (22941) SS BOND : bond 0.00512 ( 18) SS BOND : angle 1.48863 ( 36) hydrogen bonds : bond 0.04073 ( 659) hydrogen bonds : angle 4.55909 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 373 time to evaluate : 0.584 Fit side-chains REVERT: A 131 THR cc_start: 0.8637 (m) cc_final: 0.8258 (p) REVERT: A 197 LYS cc_start: 0.8288 (ptpt) cc_final: 0.8067 (ptpt) REVERT: B 22 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: B 97 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7366 (mp0) REVERT: B 119 TYR cc_start: 0.8629 (t80) cc_final: 0.8213 (t80) REVERT: B 123 LYS cc_start: 0.8731 (tttp) cc_final: 0.8389 (tttm) REVERT: B 132 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6795 (mm-30) REVERT: B 135 ASN cc_start: 0.7600 (t0) cc_final: 0.7317 (t0) REVERT: B 143 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8186 (mmmm) REVERT: C 106 GLU cc_start: 0.7776 (mp0) cc_final: 0.7315 (mp0) REVERT: C 274 MET cc_start: 0.6867 (tmm) cc_final: 0.6530 (tmm) REVERT: E 203 SER cc_start: 0.8610 (m) cc_final: 0.8339 (p) REVERT: E 211 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7309 (ttp80) REVERT: E 281 CYS cc_start: 0.7077 (t) cc_final: 0.6666 (t) REVERT: H 5 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: H 79 SER cc_start: 0.8225 (t) cc_final: 0.8021 (m) REVERT: H 100 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8191 (t0) REVERT: H 110 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7850 (t) REVERT: I 4 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8464 (mp) REVERT: I 20 LEU cc_start: 0.8727 (mp) cc_final: 0.8450 (mt) REVERT: I 68 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8460 (m) REVERT: J 69 THR cc_start: 0.8399 (p) cc_final: 0.7987 (m) REVERT: L 3 GLN cc_start: 0.7790 (mp10) cc_final: 0.7454 (mp10) REVERT: L 79 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7129 (mp-120) REVERT: N 5 THR cc_start: 0.8258 (m) cc_final: 0.7930 (p) REVERT: N 77 SER cc_start: 0.7512 (p) cc_final: 0.7312 (p) outliers start: 66 outliers final: 39 residues processed: 405 average time/residue: 0.6187 time to fit residues: 276.6268 Evaluate side-chains 418 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 137 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 197 optimal weight: 0.0030 chunk 39 optimal weight: 0.5980 chunk 190 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 192 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 125 GLN D 43 ASN F 125 GLN F 135 ASN L 79 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104854 restraints weight = 24350.443| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.76 r_work: 0.3332 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16895 Z= 0.149 Angle : 0.557 11.963 22977 Z= 0.285 Chirality : 0.042 0.184 2516 Planarity : 0.004 0.046 2955 Dihedral : 4.831 82.601 2339 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.19 % Allowed : 27.95 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2124 helix: 2.92 (0.27), residues: 363 sheet: 1.04 (0.24), residues: 505 loop : -1.02 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 310 TYR 0.011 0.001 TYR I 50 PHE 0.010 0.001 PHE C 245 TRP 0.012 0.001 TRP F 21 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00350 (16877) covalent geometry : angle 0.55434 (22941) SS BOND : bond 0.00531 ( 18) SS BOND : angle 1.46842 ( 36) hydrogen bonds : bond 0.04137 ( 659) hydrogen bonds : angle 4.55766 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 0.597 Fit side-chains REVERT: A 131 THR cc_start: 0.8631 (m) cc_final: 0.8256 (p) REVERT: A 197 LYS cc_start: 0.8278 (ptpt) cc_final: 0.8022 (ptpt) REVERT: B 22 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: B 97 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7359 (mp0) REVERT: B 123 LYS cc_start: 0.8727 (tttp) cc_final: 0.8397 (tttm) REVERT: B 132 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: B 143 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8194 (mmmm) REVERT: C 274 MET cc_start: 0.6868 (tmm) cc_final: 0.6522 (tmm) REVERT: D 101 LEU cc_start: 0.8030 (mp) cc_final: 0.7742 (mt) REVERT: E 203 SER cc_start: 0.8587 (m) cc_final: 0.8342 (p) REVERT: E 211 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7320 (ttp80) REVERT: E 281 CYS cc_start: 0.7081 (t) cc_final: 0.6665 (t) REVERT: F 131 LYS cc_start: 0.8355 (tttm) cc_final: 0.8145 (tttm) REVERT: H 5 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: H 79 SER cc_start: 0.8228 (t) cc_final: 0.8026 (m) REVERT: H 110 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7856 (t) REVERT: I 4 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8466 (mp) REVERT: I 20 LEU cc_start: 0.8712 (mp) cc_final: 0.8454 (mt) REVERT: I 68 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8476 (m) REVERT: J 69 THR cc_start: 0.8434 (p) cc_final: 0.8023 (m) REVERT: L 3 GLN cc_start: 0.7793 (mp10) cc_final: 0.7462 (mp10) REVERT: L 79 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: N 5 THR cc_start: 0.8263 (m) cc_final: 0.7945 (p) outliers start: 56 outliers final: 37 residues processed: 406 average time/residue: 0.6215 time to fit residues: 278.6397 Evaluate side-chains 417 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 372 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 0.0980 chunk 125 optimal weight: 0.3980 chunk 191 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 125 GLN D 43 ASN F 125 GLN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105510 restraints weight = 24236.717| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.76 r_work: 0.3343 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16895 Z= 0.119 Angle : 0.546 11.136 22977 Z= 0.279 Chirality : 0.041 0.171 2516 Planarity : 0.004 0.047 2955 Dihedral : 4.764 86.601 2339 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.68 % Allowed : 28.35 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2124 helix: 3.04 (0.27), residues: 363 sheet: 1.11 (0.24), residues: 502 loop : -0.97 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.013 0.001 TYR F 22 PHE 0.010 0.001 PHE B 9 TRP 0.011 0.001 TRP F 21 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00276 (16877) covalent geometry : angle 0.54361 (22941) SS BOND : bond 0.00471 ( 18) SS BOND : angle 1.36303 ( 36) hydrogen bonds : bond 0.03922 ( 659) hydrogen bonds : angle 4.50499 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 0.638 Fit side-chains REVERT: A 131 THR cc_start: 0.8626 (m) cc_final: 0.8260 (p) REVERT: A 197 LYS cc_start: 0.8237 (ptpt) cc_final: 0.7971 (ptpt) REVERT: B 22 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: B 97 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7315 (mp0) REVERT: B 119 TYR cc_start: 0.8618 (t80) cc_final: 0.8191 (t80) REVERT: B 123 LYS cc_start: 0.8730 (tttp) cc_final: 0.8394 (tttm) REVERT: B 132 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: B 143 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8182 (mmmm) REVERT: C 274 MET cc_start: 0.6905 (tmm) cc_final: 0.6558 (tmm) REVERT: E 203 SER cc_start: 0.8567 (m) cc_final: 0.8334 (p) REVERT: E 281 CYS cc_start: 0.7077 (t) cc_final: 0.6666 (t) REVERT: H 5 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: H 79 SER cc_start: 0.8152 (t) cc_final: 0.7950 (m) REVERT: H 100 PHE cc_start: 0.8686 (m-10) cc_final: 0.8440 (m-10) REVERT: H 110 THR cc_start: 0.8263 (p) cc_final: 0.7848 (t) REVERT: I 4 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8463 (mp) REVERT: I 20 LEU cc_start: 0.8686 (mp) cc_final: 0.8437 (mt) REVERT: I 68 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8479 (m) REVERT: J 69 THR cc_start: 0.8425 (p) cc_final: 0.7994 (m) REVERT: L 3 GLN cc_start: 0.7792 (mp10) cc_final: 0.7459 (mp10) REVERT: L 79 GLN cc_start: 0.7899 (mp10) cc_final: 0.7015 (mp10) REVERT: N 5 THR cc_start: 0.8215 (m) cc_final: 0.7898 (p) outliers start: 47 outliers final: 28 residues processed: 397 average time/residue: 0.6076 time to fit residues: 266.8263 Evaluate side-chains 404 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 65 optimal weight: 1.9990 chunk 177 optimal weight: 0.3980 chunk 207 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 172 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 186 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN D 43 ASN F 125 GLN F 135 ASN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105460 restraints weight = 24393.011| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.77 r_work: 0.3351 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16895 Z= 0.119 Angle : 0.557 11.880 22977 Z= 0.283 Chirality : 0.041 0.162 2516 Planarity : 0.004 0.047 2955 Dihedral : 4.331 42.111 2336 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.28 % Allowed : 29.04 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2124 helix: 3.05 (0.27), residues: 363 sheet: 1.14 (0.24), residues: 502 loop : -0.94 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 76 TYR 0.014 0.001 TYR F 22 PHE 0.010 0.001 PHE B 9 TRP 0.012 0.001 TRP F 21 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00276 (16877) covalent geometry : angle 0.55519 (22941) SS BOND : bond 0.00468 ( 18) SS BOND : angle 1.33528 ( 36) hydrogen bonds : bond 0.03902 ( 659) hydrogen bonds : angle 4.50197 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6705.17 seconds wall clock time: 114 minutes 38.69 seconds (6878.69 seconds total)