Starting phenix.real_space_refine on Thu Sep 18 14:09:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu7_45930/09_2025/9cu7_45930_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu7_45930/09_2025/9cu7_45930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cu7_45930/09_2025/9cu7_45930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu7_45930/09_2025/9cu7_45930.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu7_45930/09_2025/9cu7_45930_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu7_45930/09_2025/9cu7_45930_neut.cif" } resolution = 2.82 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 78 5.16 5 C 10667 2.51 5 N 2924 2.21 5 O 3244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16913 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 950 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 957 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 957 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "N" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2505 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2505 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2505 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1347 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1347 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1347 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 3.93, per 1000 atoms: 0.23 Number of scatterers: 16913 At special positions: 0 Unit cell: (131.192, 129.605, 146.004, 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 78 16.00 O 3244 8.00 N 2924 7.00 C 10667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.05 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.04 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 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.04 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.04 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 825.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 53 sheets defined 19.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.686A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.757A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.677A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 126 removed outlier: 4.054A pdb=" N SER A 126 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 125 through 126 removed outlier: 3.931A pdb=" N SER E 126 " --> pdb=" O LYS E 125A" (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.732A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.834A pdb=" N LEU B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.889A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 170 removed outlier: 3.820A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 59 removed outlier: 3.599A pdb=" N LYS F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 170 removed outlier: 3.860A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.712A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.102A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.688A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.063A pdb=" N ILE I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.744A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.052A pdb=" N ILE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.742A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.778A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.599A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER M 67 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.623A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AB7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.731A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.681A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.650A pdb=" N PHE B 138 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.053A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.475A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.602A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.569A pdb=" N SER A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER A 138 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N GLU A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AD1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AD3, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AD5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.641A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.682A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 115 through 122 removed outlier: 3.543A pdb=" N SER C 117 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AE2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.875A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AE4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AE5, first strand: chain 'C' and resid 286 through 288 Processing sheet with id=AE6, first strand: chain 'F' and resid 31 through 36 Processing sheet with id=AE7, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AE8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AF1, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.257A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.349A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 115 through 122 removed outlier: 3.508A pdb=" N SER E 117 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 119 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AF5, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.785A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AF7, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AF8, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.571A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5562 1.35 - 1.47: 4468 1.47 - 1.60: 7180 1.60 - 1.72: 0 1.72 - 1.85: 108 Bond restraints: 17318 Sorted by residual: bond pdb=" CA SER M 67 " pdb=" CB SER M 67 " ideal model delta sigma weight residual 1.532 1.464 0.068 1.68e-02 3.54e+03 1.64e+01 bond pdb=" CA SER L 67 " pdb=" CB SER L 67 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.65e-02 3.67e+03 1.06e+01 bond pdb=" N VAL H 100C" pdb=" CA VAL H 100C" ideal model delta sigma weight residual 1.460 1.495 -0.036 1.10e-02 8.26e+03 1.06e+01 bond pdb=" N VAL I 100D" pdb=" CA VAL I 100D" ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" N VAL J 100 " pdb=" CA VAL J 100 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.08e-02 8.57e+03 9.96e+00 ... (remaining 17313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 23275 2.64 - 5.28: 208 5.28 - 7.92: 17 7.92 - 10.56: 2 10.56 - 13.20: 1 Bond angle restraints: 23503 Sorted by residual: angle pdb=" C CYS B 137 " pdb=" CA CYS B 137 " pdb=" CB CYS B 137 " ideal model delta sigma weight residual 113.19 99.99 13.20 2.37e+00 1.78e-01 3.10e+01 angle pdb=" CA PHE L 71 " pdb=" CB PHE L 71 " pdb=" CG PHE L 71 " ideal model delta sigma weight residual 113.80 118.92 -5.12 1.00e+00 1.00e+00 2.63e+01 angle pdb=" N CYS B 137 " pdb=" CA CYS B 137 " pdb=" C CYS B 137 " ideal model delta sigma weight residual 108.34 114.32 -5.98 1.31e+00 5.83e-01 2.08e+01 angle pdb=" CA GLY M 66 " pdb=" C GLY M 66 " pdb=" O GLY M 66 " ideal model delta sigma weight residual 122.33 118.71 3.62 8.10e-01 1.52e+00 2.00e+01 angle pdb=" N THR M 69 " pdb=" CA THR M 69 " pdb=" CB THR M 69 " ideal model delta sigma weight residual 110.59 104.65 5.94 1.33e+00 5.65e-01 1.99e+01 ... (remaining 23498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8652 17.92 - 35.84: 1115 35.84 - 53.76: 379 53.76 - 71.68: 74 71.68 - 89.60: 28 Dihedral angle restraints: 10248 sinusoidal: 4014 harmonic: 6234 Sorted by residual: dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -12.20 -73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS E 52 " pdb=" SG CYS E 52 " pdb=" SG CYS E 277 " pdb=" CB CYS E 277 " ideal model delta sinusoidal sigma weight residual -86.00 -21.25 -64.75 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 155.13 -62.13 1 1.00e+01 1.00e-02 5.11e+01 ... (remaining 10245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1686 0.040 - 0.080: 631 0.080 - 0.120: 187 0.120 - 0.159: 20 0.159 - 0.199: 8 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CA VAL H 100 " pdb=" N VAL H 100 " pdb=" C VAL H 100 " pdb=" CB VAL H 100 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA VAL J 100 " pdb=" N VAL J 100 " pdb=" C VAL J 100 " pdb=" CB VAL J 100 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA VAL I 100 " pdb=" N VAL I 100 " pdb=" C VAL I 100 " pdb=" CB VAL I 100 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 2529 not shown) Planarity restraints: 3050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 71 " 0.811 9.50e-02 1.11e+02 3.64e-01 8.07e+01 pdb=" NE ARG I 71 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG I 71 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG I 71 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG I 71 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 94 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C TYR B 94 " 0.040 2.00e-02 2.50e+03 pdb=" O TYR B 94 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 95 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 36 " 0.019 2.00e-02 2.50e+03 1.47e-02 5.44e+00 pdb=" CG TRP I 36 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP I 36 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP I 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 36 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP I 36 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP I 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 36 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 36 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP I 36 " 0.005 2.00e-02 2.50e+03 ... (remaining 3047 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2186 2.75 - 3.29: 15193 3.29 - 3.82: 28611 3.82 - 4.36: 33674 4.36 - 4.90: 60335 Nonbonded interactions: 139999 Sorted by model distance: nonbonded pdb=" OD1 ASN B 128 " pdb=" OH TYR B 159 " model vdw 2.209 3.040 nonbonded pdb=" O SER J 82B" pdb=" OG SER J 82B" model vdw 2.218 3.040 nonbonded pdb=" NZ LYS F 51 " pdb=" OE1 GLU F 103 " model vdw 2.223 3.120 nonbonded pdb=" OD1 ASN D 128 " pdb=" OH TYR D 159 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP J 100I" pdb=" NZ LYS N 50 " model vdw 2.228 3.120 ... (remaining 139994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 113)) selection = (chain 'J' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 113)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 34.430 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: 0.670 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.006 0.068 17342 Z= 0.275 Angle : 0.616 13.203 23551 Z= 0.350 Chirality : 0.045 0.199 2532 Planarity : 0.008 0.364 3050 Dihedral : 18.224 89.602 6204 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.76 % Allowed : 31.56 % Favored : 63.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.45 (0.17), residues: 2148 helix: 1.32 (0.27), residues: 381 sheet: -0.38 (0.21), residues: 549 loop : -0.75 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 71 TYR 0.018 0.002 TYR E 17 PHE 0.020 0.002 PHE C 118 TRP 0.037 0.002 TRP I 36 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00569 (17318) covalent geometry : angle 0.61091 (23503) SS BOND : bond 0.00547 ( 24) SS BOND : angle 1.86326 ( 48) hydrogen bonds : bond 0.13389 ( 696) hydrogen bonds : angle 7.46177 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 441 time to evaluate : 0.667 Fit side-chains REVERT: L 82 ASP cc_start: 0.7538 (m-30) cc_final: 0.7277 (m-30) REVERT: A 80 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7597 (mp) REVERT: A 116 SER cc_start: 0.8010 (t) cc_final: 0.7447 (p) REVERT: A 117 SER cc_start: 0.7999 (p) cc_final: 0.7661 (m) REVERT: C 107 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7435 (tm-30) REVERT: C 176 VAL cc_start: 0.8455 (t) cc_final: 0.8197 (p) REVERT: E 50 LYS cc_start: 0.8033 (mttm) cc_final: 0.7654 (mttm) REVERT: E 107 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7641 (tm-30) REVERT: E 149 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8078 (mtpp) REVERT: E 246 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: E 280 LYS cc_start: 0.8021 (mttt) cc_final: 0.7728 (tttt) REVERT: B 51 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7848 (tttp) REVERT: B 53 ASN cc_start: 0.8712 (m-40) cc_final: 0.8423 (m110) REVERT: B 59 MET cc_start: 0.8159 (ptp) cc_final: 0.7899 (mtm) REVERT: B 103 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7172 (mm-30) REVERT: B 149 MET cc_start: 0.7625 (mmt) cc_final: 0.7422 (mmp) REVERT: D 131 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8094 (ttmm) REVERT: D 132 GLU cc_start: 0.7497 (tt0) cc_final: 0.7153 (tt0) REVERT: F 53 ASN cc_start: 0.8460 (m-40) cc_final: 0.8178 (m110) REVERT: F 143 LYS cc_start: 0.8328 (mttp) cc_final: 0.7993 (mtpp) REVERT: F 149 MET cc_start: 0.7497 (mmt) cc_final: 0.7293 (mmp) outliers start: 87 outliers final: 70 residues processed: 480 average time/residue: 0.6449 time to fit residues: 343.0207 Evaluate side-chains 513 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 439 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 145 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN J 97 GLN L 38 GLN A 95 ASN A 170 ASN C 129 ASN C 271 ASN E 41 ASN E 47 HIS E 269 ASN E 271 ASN B 43 ASN B 169 ASN D 50 ASN F 50 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109998 restraints weight = 24149.002| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.98 r_work: 0.3326 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17342 Z= 0.159 Angle : 0.505 6.674 23551 Z= 0.269 Chirality : 0.042 0.143 2532 Planarity : 0.004 0.048 3050 Dihedral : 7.117 58.226 2479 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.62 % Allowed : 26.97 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.03 (0.18), residues: 2148 helix: 2.19 (0.27), residues: 384 sheet: -0.06 (0.22), residues: 519 loop : -0.70 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 229 TYR 0.013 0.001 TYR I 91 PHE 0.017 0.002 PHE A 118 TRP 0.016 0.001 TRP I 36 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00365 (17318) covalent geometry : angle 0.50213 (23503) SS BOND : bond 0.00409 ( 24) SS BOND : angle 1.21568 ( 48) hydrogen bonds : bond 0.04371 ( 696) hydrogen bonds : angle 5.24271 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 451 time to evaluate : 0.624 Fit side-chains REVERT: L 82 ASP cc_start: 0.7644 (m-30) cc_final: 0.7383 (m-30) REVERT: M 4 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7770 (mtm) REVERT: N 23 CYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6703 (t) REVERT: A 53 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7731 (mtt90) REVERT: A 149 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: C 107 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7265 (tm-30) REVERT: C 176 VAL cc_start: 0.8357 (t) cc_final: 0.8105 (p) REVERT: E 117 SER cc_start: 0.7939 (m) cc_final: 0.7644 (p) REVERT: E 167 SER cc_start: 0.8358 (t) cc_final: 0.8078 (m) REVERT: E 246 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: B 53 ASN cc_start: 0.8693 (m-40) cc_final: 0.8344 (m110) REVERT: B 103 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 149 MET cc_start: 0.7740 (mmt) cc_final: 0.7500 (mmp) REVERT: D 105 GLU cc_start: 0.7594 (tp30) cc_final: 0.7301 (tp30) REVERT: D 132 GLU cc_start: 0.7427 (tt0) cc_final: 0.7124 (tt0) REVERT: F 53 ASN cc_start: 0.8404 (m-40) cc_final: 0.8087 (m110) REVERT: F 143 LYS cc_start: 0.8227 (mttp) cc_final: 0.7883 (mtpp) REVERT: F 149 MET cc_start: 0.7547 (mmt) cc_final: 0.7234 (mmp) REVERT: F 150 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: F 164 GLU cc_start: 0.7363 (tp30) cc_final: 0.7063 (tp30) outliers start: 121 outliers final: 54 residues processed: 518 average time/residue: 0.6001 time to fit residues: 346.0686 Evaluate side-chains 504 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 445 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 200 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN A 95 ASN A 170 ASN C 129 ASN C 271 ASN E 41 ASN E 271 ASN B 43 ASN D 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112941 restraints weight = 24162.120| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.05 r_work: 0.3297 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17342 Z= 0.213 Angle : 0.535 7.400 23551 Z= 0.282 Chirality : 0.043 0.144 2532 Planarity : 0.004 0.049 3050 Dihedral : 5.511 52.288 2381 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.84 % Allowed : 27.13 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.00 (0.18), residues: 2148 helix: 2.26 (0.27), residues: 381 sheet: -0.00 (0.22), residues: 519 loop : -0.71 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 229 TYR 0.017 0.001 TYR H 91 PHE 0.022 0.002 PHE C 118 TRP 0.011 0.001 TRP I 36 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00495 (17318) covalent geometry : angle 0.53090 (23503) SS BOND : bond 0.00440 ( 24) SS BOND : angle 1.51517 ( 48) hydrogen bonds : bond 0.04619 ( 696) hydrogen bonds : angle 5.18533 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 451 time to evaluate : 0.622 Fit side-chains REVERT: I 52 SER cc_start: 0.8385 (m) cc_final: 0.8172 (t) REVERT: L 82 ASP cc_start: 0.7633 (m-30) cc_final: 0.7370 (m-30) REVERT: A 53 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7682 (mtt90) REVERT: A 149 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: A 176 VAL cc_start: 0.8332 (t) cc_final: 0.8090 (t) REVERT: C 107 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7315 (tm-30) REVERT: C 176 VAL cc_start: 0.8351 (t) cc_final: 0.8086 (p) REVERT: E 117 SER cc_start: 0.7942 (m) cc_final: 0.7674 (p) REVERT: E 167 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8123 (m) REVERT: E 246 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 53 ASN cc_start: 0.8751 (m-40) cc_final: 0.8471 (m110) REVERT: B 149 MET cc_start: 0.7779 (mmt) cc_final: 0.7524 (mmp) REVERT: D 105 GLU cc_start: 0.7650 (tp30) cc_final: 0.7370 (tp30) REVERT: D 132 GLU cc_start: 0.7464 (tt0) cc_final: 0.7179 (tt0) REVERT: F 53 ASN cc_start: 0.8447 (m-40) cc_final: 0.8152 (m110) REVERT: F 143 LYS cc_start: 0.8218 (mttp) cc_final: 0.7889 (mtpp) REVERT: F 149 MET cc_start: 0.7609 (mmt) cc_final: 0.7361 (mmp) REVERT: F 150 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: F 164 GLU cc_start: 0.7439 (tp30) cc_final: 0.7142 (tp30) outliers start: 125 outliers final: 69 residues processed: 517 average time/residue: 0.6199 time to fit residues: 356.6897 Evaluate side-chains 524 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 451 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 14 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 150 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 193 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 97 GLN L 38 GLN A 95 ASN A 170 ASN C 129 ASN C 271 ASN E 41 ASN E 269 ASN E 271 ASN B 43 ASN F 50 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113221 restraints weight = 24232.725| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.02 r_work: 0.3300 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17342 Z= 0.164 Angle : 0.513 8.181 23551 Z= 0.270 Chirality : 0.042 0.148 2532 Planarity : 0.004 0.049 3050 Dihedral : 5.290 55.537 2378 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.96 % Allowed : 28.34 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.05 (0.18), residues: 2148 helix: 2.30 (0.27), residues: 384 sheet: 0.04 (0.22), residues: 519 loop : -0.69 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 229 TYR 0.013 0.001 TYR J 91 PHE 0.018 0.001 PHE C 118 TRP 0.012 0.001 TRP I 36 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00379 (17318) covalent geometry : angle 0.50835 (23503) SS BOND : bond 0.00408 ( 24) SS BOND : angle 1.58409 ( 48) hydrogen bonds : bond 0.04274 ( 696) hydrogen bonds : angle 5.02287 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 451 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: L 6 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8141 (m-70) REVERT: L 82 ASP cc_start: 0.7640 (m-30) cc_final: 0.7371 (m-30) REVERT: M 74 THR cc_start: 0.8640 (p) cc_final: 0.8397 (p) REVERT: A 53 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.7662 (mtt90) REVERT: A 80 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7645 (mp) REVERT: A 149 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: A 197 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8747 (ttmm) REVERT: A 237 LEU cc_start: 0.8162 (tp) cc_final: 0.7959 (mt) REVERT: C 107 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7304 (tm-30) REVERT: C 176 VAL cc_start: 0.8348 (t) cc_final: 0.8083 (p) REVERT: E 50 LYS cc_start: 0.8085 (mttm) cc_final: 0.7679 (mttm) REVERT: E 117 SER cc_start: 0.7911 (m) cc_final: 0.7644 (p) REVERT: E 167 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8075 (m) REVERT: E 280 LYS cc_start: 0.8432 (tttt) cc_final: 0.8170 (tttt) REVERT: B 51 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8084 (tttp) REVERT: B 53 ASN cc_start: 0.8700 (m-40) cc_final: 0.8360 (m110) REVERT: B 149 MET cc_start: 0.7777 (mmt) cc_final: 0.7522 (mmp) REVERT: D 77 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8062 (mtp) REVERT: D 105 GLU cc_start: 0.7611 (tp30) cc_final: 0.7347 (tp30) REVERT: D 132 GLU cc_start: 0.7419 (tt0) cc_final: 0.7150 (tt0) REVERT: D 149 MET cc_start: 0.7714 (mmt) cc_final: 0.7489 (mmp) REVERT: F 53 ASN cc_start: 0.8431 (m-40) cc_final: 0.8128 (m110) REVERT: F 77 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7846 (tpt) REVERT: F 143 LYS cc_start: 0.8173 (mttp) cc_final: 0.7842 (mtpp) REVERT: F 149 MET cc_start: 0.7591 (mmt) cc_final: 0.7350 (mmp) REVERT: F 150 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7234 (mp0) outliers start: 109 outliers final: 63 residues processed: 499 average time/residue: 0.6657 time to fit residues: 367.9206 Evaluate side-chains 512 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 441 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 6 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 168 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 65 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 95 ASN A 170 ASN C 129 ASN C 271 ASN E 271 ASN B 43 ASN F 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109271 restraints weight = 24320.594| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.97 r_work: 0.3304 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17342 Z= 0.185 Angle : 0.526 9.682 23551 Z= 0.277 Chirality : 0.043 0.163 2532 Planarity : 0.004 0.049 3050 Dihedral : 5.016 58.691 2370 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.73 % Allowed : 27.63 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.03 (0.18), residues: 2148 helix: 2.27 (0.27), residues: 384 sheet: 0.05 (0.22), residues: 519 loop : -0.72 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 229 TYR 0.017 0.001 TYR H 91 PHE 0.020 0.002 PHE C 118 TRP 0.015 0.001 TRP I 36 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00429 (17318) covalent geometry : angle 0.52105 (23503) SS BOND : bond 0.00500 ( 24) SS BOND : angle 1.66174 ( 48) hydrogen bonds : bond 0.04355 ( 696) hydrogen bonds : angle 5.01473 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 457 time to evaluate : 0.648 Fit side-chains REVERT: H 29 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7818 (mp) REVERT: J 81 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: L 6 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8145 (m-70) REVERT: L 82 ASP cc_start: 0.7616 (m-30) cc_final: 0.7346 (m-30) REVERT: M 4 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7864 (mtp) REVERT: A 53 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7714 (mtt90) REVERT: A 80 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7645 (mp) REVERT: A 149 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8078 (mtpp) REVERT: C 82 ARG cc_start: 0.8313 (mtp180) cc_final: 0.8059 (mtp180) REVERT: C 107 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7309 (tm-30) REVERT: C 176 VAL cc_start: 0.8354 (t) cc_final: 0.8090 (p) REVERT: E 50 LYS cc_start: 0.8089 (mttm) cc_final: 0.7672 (mttm) REVERT: E 61 LEU cc_start: 0.7925 (mt) cc_final: 0.7582 (mp) REVERT: E 117 SER cc_start: 0.7899 (m) cc_final: 0.7628 (p) REVERT: E 167 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8077 (m) REVERT: E 207 SER cc_start: 0.7580 (OUTLIER) cc_final: 0.7161 (m) REVERT: E 246 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: E 280 LYS cc_start: 0.8484 (tttt) cc_final: 0.8208 (tttt) REVERT: B 51 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8097 (tttp) REVERT: B 53 ASN cc_start: 0.8690 (m-40) cc_final: 0.8364 (m110) REVERT: B 149 MET cc_start: 0.7758 (mmt) cc_final: 0.7498 (mmp) REVERT: D 105 GLU cc_start: 0.7583 (tp30) cc_final: 0.7315 (tp30) REVERT: D 132 GLU cc_start: 0.7406 (tt0) cc_final: 0.7148 (tt0) REVERT: F 53 ASN cc_start: 0.8428 (m-40) cc_final: 0.8127 (m110) REVERT: F 143 LYS cc_start: 0.8204 (mttp) cc_final: 0.7861 (mtpp) REVERT: F 149 MET cc_start: 0.7570 (mmt) cc_final: 0.7320 (mmp) REVERT: F 150 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7226 (mp0) outliers start: 123 outliers final: 69 residues processed: 520 average time/residue: 0.6506 time to fit residues: 375.8998 Evaluate side-chains 535 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 455 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 6 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 24 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 185 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 191 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 6 HIS A 95 ASN A 170 ASN C 129 ASN E 41 ASN E 271 ASN B 43 ASN B 169 ASN F 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109748 restraints weight = 24181.750| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.97 r_work: 0.3309 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17342 Z= 0.180 Angle : 0.534 9.967 23551 Z= 0.280 Chirality : 0.043 0.147 2532 Planarity : 0.004 0.049 3050 Dihedral : 4.861 51.334 2368 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.18 % Allowed : 28.39 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.01 (0.18), residues: 2148 helix: 2.22 (0.27), residues: 384 sheet: 0.08 (0.22), residues: 519 loop : -0.74 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 220 TYR 0.017 0.001 TYR J 91 PHE 0.020 0.002 PHE C 118 TRP 0.015 0.001 TRP I 36 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00417 (17318) covalent geometry : angle 0.53015 (23503) SS BOND : bond 0.00475 ( 24) SS BOND : angle 1.47363 ( 48) hydrogen bonds : bond 0.04326 ( 696) hydrogen bonds : angle 4.99554 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 457 time to evaluate : 0.792 Fit side-chains REVERT: J 81 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: L 6 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8144 (m-70) REVERT: L 82 ASP cc_start: 0.7663 (m-30) cc_final: 0.7386 (m-30) REVERT: A 53 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7707 (mtt90) REVERT: A 80 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 119 GLU cc_start: 0.7521 (tt0) cc_final: 0.7299 (tt0) REVERT: A 149 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: C 107 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7281 (tm-30) REVERT: C 176 VAL cc_start: 0.8357 (t) cc_final: 0.8104 (p) REVERT: E 50 LYS cc_start: 0.8078 (mttm) cc_final: 0.7718 (mttm) REVERT: E 54 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7911 (mp) REVERT: E 61 LEU cc_start: 0.7971 (mt) cc_final: 0.7624 (mp) REVERT: E 117 SER cc_start: 0.7920 (m) cc_final: 0.7673 (p) REVERT: E 207 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7155 (m) REVERT: E 246 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: E 280 LYS cc_start: 0.8495 (tttt) cc_final: 0.8216 (tttt) REVERT: B 51 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8099 (tttp) REVERT: B 53 ASN cc_start: 0.8702 (m-40) cc_final: 0.8369 (m110) REVERT: B 149 MET cc_start: 0.7760 (mmt) cc_final: 0.7495 (mmp) REVERT: D 105 GLU cc_start: 0.7623 (tp30) cc_final: 0.7353 (tp30) REVERT: D 132 GLU cc_start: 0.7421 (tt0) cc_final: 0.7187 (tt0) REVERT: D 149 MET cc_start: 0.7649 (mmt) cc_final: 0.7448 (mmp) REVERT: F 53 ASN cc_start: 0.8441 (m-40) cc_final: 0.8142 (m110) REVERT: F 143 LYS cc_start: 0.8203 (mttp) cc_final: 0.7846 (mtpp) REVERT: F 149 MET cc_start: 0.7544 (mmt) cc_final: 0.7289 (mmp) REVERT: F 150 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7243 (mp0) outliers start: 113 outliers final: 74 residues processed: 512 average time/residue: 0.6692 time to fit residues: 380.1176 Evaluate side-chains 532 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 449 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 6 HIS Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 146 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 205 optimal weight: 0.3980 chunk 170 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 95 ASN A 170 ASN C 129 ASN C 271 ASN E 271 ASN B 43 ASN B 169 ASN ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109383 restraints weight = 24223.222| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.98 r_work: 0.3306 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17342 Z= 0.180 Angle : 0.534 9.619 23551 Z= 0.280 Chirality : 0.043 0.142 2532 Planarity : 0.004 0.049 3050 Dihedral : 4.866 51.523 2368 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.35 % Allowed : 28.50 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.02 (0.18), residues: 2148 helix: 2.19 (0.27), residues: 384 sheet: 0.11 (0.22), residues: 519 loop : -0.73 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 229 TYR 0.016 0.001 TYR J 91 PHE 0.020 0.002 PHE C 118 TRP 0.019 0.001 TRP I 36 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00418 (17318) covalent geometry : angle 0.53080 (23503) SS BOND : bond 0.00478 ( 24) SS BOND : angle 1.40617 ( 48) hydrogen bonds : bond 0.04328 ( 696) hydrogen bonds : angle 4.99284 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 448 time to evaluate : 0.627 Fit side-chains REVERT: J 81 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: L 6 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.8139 (m-70) REVERT: L 82 ASP cc_start: 0.7656 (m-30) cc_final: 0.7391 (m-30) REVERT: A 53 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7732 (mtt90) REVERT: A 61 LEU cc_start: 0.8126 (mt) cc_final: 0.7923 (mp) REVERT: A 80 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7645 (mp) REVERT: A 149 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8070 (mtpp) REVERT: A 237 LEU cc_start: 0.8166 (tp) cc_final: 0.7965 (mt) REVERT: C 107 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7288 (tm-30) REVERT: C 176 VAL cc_start: 0.8356 (t) cc_final: 0.8104 (p) REVERT: E 50 LYS cc_start: 0.8048 (mttm) cc_final: 0.7695 (mttm) REVERT: E 117 SER cc_start: 0.7932 (m) cc_final: 0.7686 (p) REVERT: E 207 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7146 (m) REVERT: E 246 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: E 280 LYS cc_start: 0.8498 (tttt) cc_final: 0.8220 (tttt) REVERT: B 51 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8093 (tttp) REVERT: B 53 ASN cc_start: 0.8709 (m-40) cc_final: 0.8379 (m110) REVERT: B 149 MET cc_start: 0.7761 (mmt) cc_final: 0.7500 (mmp) REVERT: D 105 GLU cc_start: 0.7635 (tp30) cc_final: 0.7370 (tp30) REVERT: D 132 GLU cc_start: 0.7436 (tt0) cc_final: 0.7200 (tt0) REVERT: F 53 ASN cc_start: 0.8440 (m-40) cc_final: 0.8151 (m110) REVERT: F 143 LYS cc_start: 0.8212 (mttp) cc_final: 0.7856 (mtpp) REVERT: F 149 MET cc_start: 0.7553 (mmt) cc_final: 0.7299 (mmp) REVERT: F 150 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7241 (mp0) outliers start: 116 outliers final: 81 residues processed: 504 average time/residue: 0.6733 time to fit residues: 375.9872 Evaluate side-chains 529 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 440 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 6 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 38 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 161 optimal weight: 0.0570 chunk 109 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 95 ASN A 170 ASN C 129 ASN C 271 ASN E 271 ASN B 43 ASN B 169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109231 restraints weight = 24365.292| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.99 r_work: 0.3304 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17342 Z= 0.182 Angle : 0.541 9.998 23551 Z= 0.282 Chirality : 0.043 0.142 2532 Planarity : 0.004 0.051 3050 Dihedral : 4.776 51.588 2366 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.02 % Allowed : 28.50 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.02 (0.18), residues: 2148 helix: 2.20 (0.27), residues: 384 sheet: 0.10 (0.22), residues: 519 loop : -0.73 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 229 TYR 0.017 0.001 TYR C 17 PHE 0.020 0.002 PHE C 118 TRP 0.024 0.001 TRP I 36 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00423 (17318) covalent geometry : angle 0.53742 (23503) SS BOND : bond 0.00482 ( 24) SS BOND : angle 1.50157 ( 48) hydrogen bonds : bond 0.04327 ( 696) hydrogen bonds : angle 5.00060 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 443 time to evaluate : 0.705 Fit side-chains REVERT: J 81 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: L 6 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8137 (m-70) REVERT: L 82 ASP cc_start: 0.7674 (m-30) cc_final: 0.7402 (m-30) REVERT: A 53 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7732 (mtt90) REVERT: A 61 LEU cc_start: 0.8123 (mt) cc_final: 0.7906 (mp) REVERT: A 80 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 119 GLU cc_start: 0.7511 (tt0) cc_final: 0.7301 (tt0) REVERT: A 149 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: A 237 LEU cc_start: 0.8158 (tp) cc_final: 0.7952 (mt) REVERT: C 107 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7275 (tm-30) REVERT: C 176 VAL cc_start: 0.8360 (t) cc_final: 0.8105 (p) REVERT: C 192 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7843 (mpp80) REVERT: E 50 LYS cc_start: 0.8056 (mttm) cc_final: 0.7716 (mttm) REVERT: E 117 SER cc_start: 0.7943 (m) cc_final: 0.7687 (p) REVERT: E 207 SER cc_start: 0.7565 (OUTLIER) cc_final: 0.7154 (m) REVERT: E 246 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: E 280 LYS cc_start: 0.8542 (tttt) cc_final: 0.8241 (tttt) REVERT: B 51 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8100 (tttp) REVERT: B 53 ASN cc_start: 0.8701 (m-40) cc_final: 0.8363 (m110) REVERT: B 149 MET cc_start: 0.7755 (mmt) cc_final: 0.7489 (mmp) REVERT: D 105 GLU cc_start: 0.7629 (tp30) cc_final: 0.7359 (tp30) REVERT: D 132 GLU cc_start: 0.7417 (tt0) cc_final: 0.7184 (tt0) REVERT: F 53 ASN cc_start: 0.8447 (m-40) cc_final: 0.8166 (m110) REVERT: F 143 LYS cc_start: 0.8212 (mttp) cc_final: 0.7856 (mtpp) REVERT: F 149 MET cc_start: 0.7531 (mmt) cc_final: 0.7277 (mmp) REVERT: F 150 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7244 (mp0) outliers start: 110 outliers final: 80 residues processed: 502 average time/residue: 0.6437 time to fit residues: 359.1786 Evaluate side-chains 529 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 441 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 6 HIS Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 127 optimal weight: 0.0020 chunk 189 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 95 ASN A 170 ASN C 129 ASN E 41 ASN E 269 ASN E 271 ASN B 43 ASN B 169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109421 restraints weight = 24211.803| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.97 r_work: 0.3303 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17342 Z= 0.190 Angle : 0.545 9.548 23551 Z= 0.286 Chirality : 0.043 0.146 2532 Planarity : 0.004 0.052 3050 Dihedral : 4.795 51.600 2366 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.80 % Allowed : 28.39 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.04 (0.18), residues: 2148 helix: 2.23 (0.27), residues: 381 sheet: 0.08 (0.22), residues: 519 loop : -0.69 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 229 TYR 0.017 0.001 TYR J 91 PHE 0.021 0.002 PHE C 118 TRP 0.028 0.001 TRP I 36 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00442 (17318) covalent geometry : angle 0.54196 (23503) SS BOND : bond 0.00474 ( 24) SS BOND : angle 1.47674 ( 48) hydrogen bonds : bond 0.04376 ( 696) hydrogen bonds : angle 5.02108 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 441 time to evaluate : 0.751 Fit side-chains REVERT: J 81 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: L 6 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8141 (m-70) REVERT: L 82 ASP cc_start: 0.7667 (m-30) cc_final: 0.7400 (m-30) REVERT: A 53 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7704 (mtt90) REVERT: A 61 LEU cc_start: 0.8122 (mt) cc_final: 0.7907 (mp) REVERT: A 80 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7654 (mp) REVERT: A 149 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: C 107 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7277 (tm-30) REVERT: C 176 VAL cc_start: 0.8357 (t) cc_final: 0.8105 (p) REVERT: E 50 LYS cc_start: 0.8031 (mttm) cc_final: 0.7735 (mttm) REVERT: E 117 SER cc_start: 0.7931 (m) cc_final: 0.7675 (p) REVERT: E 207 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7136 (m) REVERT: E 246 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: E 280 LYS cc_start: 0.8541 (tttt) cc_final: 0.8233 (tttt) REVERT: B 51 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8103 (tttp) REVERT: B 53 ASN cc_start: 0.8702 (m-40) cc_final: 0.8358 (m110) REVERT: B 149 MET cc_start: 0.7753 (mmt) cc_final: 0.7482 (mmp) REVERT: D 105 GLU cc_start: 0.7630 (tp30) cc_final: 0.7359 (tp30) REVERT: F 53 ASN cc_start: 0.8454 (m-40) cc_final: 0.8182 (m110) REVERT: F 143 LYS cc_start: 0.8222 (mttp) cc_final: 0.7869 (mtpp) REVERT: F 149 MET cc_start: 0.7543 (mmt) cc_final: 0.7293 (mmp) REVERT: F 150 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7231 (mp0) outliers start: 106 outliers final: 85 residues processed: 493 average time/residue: 0.6564 time to fit residues: 359.0851 Evaluate side-chains 532 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 439 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 6 HIS Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 80 optimal weight: 0.0470 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 134 optimal weight: 0.0170 chunk 79 optimal weight: 0.6980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 95 ASN A 170 ASN C 129 ASN C 184 HIS C 271 ASN E 269 ASN E 271 ASN B 43 ASN B 169 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110428 restraints weight = 24269.039| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.98 r_work: 0.3322 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17342 Z= 0.119 Angle : 0.502 8.751 23551 Z= 0.263 Chirality : 0.042 0.145 2532 Planarity : 0.004 0.049 3050 Dihedral : 4.558 52.475 2365 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.49 % Allowed : 29.76 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.19 (0.18), residues: 2148 helix: 2.44 (0.27), residues: 381 sheet: 0.19 (0.23), residues: 483 loop : -0.62 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 229 TYR 0.017 0.001 TYR C 17 PHE 0.013 0.001 PHE C 118 TRP 0.033 0.001 TRP I 36 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00271 (17318) covalent geometry : angle 0.49991 (23503) SS BOND : bond 0.00367 ( 24) SS BOND : angle 1.16716 ( 48) hydrogen bonds : bond 0.03865 ( 696) hydrogen bonds : angle 4.84945 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 432 time to evaluate : 0.789 Fit side-chains REVERT: J 81 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: L 6 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8086 (m-70) REVERT: L 82 ASP cc_start: 0.7642 (m-30) cc_final: 0.7375 (m-30) REVERT: N 4 MET cc_start: 0.8121 (mmm) cc_final: 0.7893 (tpp) REVERT: A 53 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7675 (mtt90) REVERT: A 80 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7653 (mp) REVERT: A 149 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8046 (mtpp) REVERT: C 44 GLU cc_start: 0.7814 (tp30) cc_final: 0.7589 (tp30) REVERT: C 107 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7292 (tm-30) REVERT: C 176 VAL cc_start: 0.8339 (t) cc_final: 0.8089 (p) REVERT: C 192 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7762 (mpp80) REVERT: E 50 LYS cc_start: 0.8012 (mttm) cc_final: 0.7681 (mttm) REVERT: E 117 SER cc_start: 0.7917 (m) cc_final: 0.7632 (p) REVERT: E 149 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7985 (mtpp) REVERT: E 207 SER cc_start: 0.7581 (OUTLIER) cc_final: 0.7208 (m) REVERT: E 246 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: E 280 LYS cc_start: 0.8540 (tttt) cc_final: 0.8225 (tttt) REVERT: B 51 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7996 (tttp) REVERT: B 53 ASN cc_start: 0.8602 (m-40) cc_final: 0.8309 (m110) REVERT: B 127 LYS cc_start: 0.8500 (mttp) cc_final: 0.8207 (mtmp) REVERT: B 149 MET cc_start: 0.7749 (mmt) cc_final: 0.7487 (mmp) REVERT: D 105 GLU cc_start: 0.7595 (tp30) cc_final: 0.7325 (tp30) REVERT: F 53 ASN cc_start: 0.8393 (m-40) cc_final: 0.8115 (m110) REVERT: F 143 LYS cc_start: 0.8232 (mttp) cc_final: 0.7868 (mtpp) REVERT: F 149 MET cc_start: 0.7563 (mmt) cc_final: 0.7318 (mmp) REVERT: F 150 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7260 (mp0) outliers start: 82 outliers final: 58 residues processed: 476 average time/residue: 0.6123 time to fit residues: 323.8325 Evaluate side-chains 495 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 429 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 6 HIS Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 138 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 0.0670 chunk 165 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 93 optimal weight: 0.1980 chunk 78 optimal weight: 0.1980 chunk 67 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 192 optimal weight: 0.0980 chunk 133 optimal weight: 1.9990 overall best weight: 0.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 95 ASN A 129 ASN A 170 ASN C 129 ASN C 271 ASN E 271 ASN B 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111307 restraints weight = 24283.297| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.98 r_work: 0.3337 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17342 Z= 0.103 Angle : 0.499 9.371 23551 Z= 0.259 Chirality : 0.042 0.141 2532 Planarity : 0.004 0.049 3050 Dihedral : 4.396 52.216 2364 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.83 % Allowed : 30.58 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: 0.33 (0.18), residues: 2148 helix: 2.45 (0.27), residues: 381 sheet: 0.48 (0.22), residues: 561 loop : -0.64 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 82 TYR 0.016 0.001 TYR C 17 PHE 0.014 0.001 PHE C 118 TRP 0.041 0.001 TRP I 36 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00232 (17318) covalent geometry : angle 0.49699 (23503) SS BOND : bond 0.00336 ( 24) SS BOND : angle 1.03684 ( 48) hydrogen bonds : bond 0.03696 ( 696) hydrogen bonds : angle 4.71921 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8774.39 seconds wall clock time: 150 minutes 7.93 seconds (9007.93 seconds total)