Starting phenix.real_space_refine on Thu Sep 18 20:06:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o62_70157/09_2025/9o62_70157_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o62_70157/09_2025/9o62_70157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o62_70157/09_2025/9o62_70157_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o62_70157/09_2025/9o62_70157_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o62_70157/09_2025/9o62_70157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o62_70157/09_2025/9o62_70157.map" } resolution = 2.03 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= 0.003 sd= 1.036 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 126 5.16 5 C 12265 2.51 5 N 3249 2.21 5 O 3736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s 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: 19376 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "B" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "C" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "D" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "E" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "F" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "G" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "H" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "I" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "J" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "K" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "L" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1275 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain: "a" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1403 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "b" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1581 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 188} Chain breaks: 5 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'PEB': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 1, 'PUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 1, 'PUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.15, per 1000 atoms: 0.27 Number of scatterers: 19376 At special positions: 0 Unit cell: (95.94, 132.02, 168.1, 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 126 16.00 O 3736 8.00 N 3249 7.00 C 12265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 91 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 95 " 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 911.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 11 sheets defined 72.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 20 through 47 removed outlier: 4.279A pdb=" N ALA A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 75 through 100 Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.855A pdb=" N TYR A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.797A pdb=" N LYS B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.531A pdb=" N ASN B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 20 through 63 removed outlier: 4.311A pdb=" N ALA C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 75 through 100 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.854A pdb=" N TYR C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 164 Processing helix chain 'D' and resid 3 through 14 Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 33 through 47 removed outlier: 3.548A pdb=" N ASN D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 102 through 109 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 20 through 47 removed outlier: 4.314A pdb=" N ALA E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SER E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 75 through 100 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 123 through 138 removed outlier: 3.899A pdb=" N TYR E 127 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 164 Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.976A pdb=" N LYS F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 33 Processing helix chain 'F' and resid 33 through 46 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 64 through 67 Processing helix chain 'F' and resid 75 through 100 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 123 through 143 Processing helix chain 'F' and resid 158 through 176 Processing helix chain 'G' and resid 3 through 16 Processing helix chain 'G' and resid 20 through 47 removed outlier: 4.312A pdb=" N ALA G 35 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 75 through 100 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 112 through 120 Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.981A pdb=" N TYR G 127 " --> pdb=" O PRO G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 164 Processing helix chain 'H' and resid 3 through 14 Processing helix chain 'H' and resid 20 through 33 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.588A pdb=" N ILE H 67 " --> pdb=" O PRO H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 75 through 100 Processing helix chain 'H' and resid 102 through 109 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'H' and resid 123 through 143 Processing helix chain 'H' and resid 158 through 176 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 20 through 63 removed outlier: 4.324A pdb=" N ALA I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA I 50 " --> pdb=" O GLY I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 75 through 100 Processing helix chain 'I' and resid 102 through 109 Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'I' and resid 123 through 138 removed outlier: 3.942A pdb=" N TYR I 127 " --> pdb=" O PRO I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.956A pdb=" N LYS J 15 " --> pdb=" O ASN J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 33 through 47 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 64 through 67 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 123 through 143 Processing helix chain 'J' and resid 158 through 176 Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 20 through 47 removed outlier: 4.364A pdb=" N ALA K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 64 through 68 Processing helix chain 'K' and resid 75 through 100 Processing helix chain 'K' and resid 102 through 109 Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'K' and resid 123 through 138 removed outlier: 3.925A pdb=" N TYR K 127 " --> pdb=" O PRO K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 164 Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.948A pdb=" N LYS L 15 " --> pdb=" O ASN L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 33 Processing helix chain 'L' and resid 33 through 46 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 64 through 67 Processing helix chain 'L' and resid 75 through 100 Processing helix chain 'L' and resid 102 through 109 Processing helix chain 'L' and resid 112 through 121 Processing helix chain 'L' and resid 123 through 143 Processing helix chain 'L' and resid 158 through 176 Processing helix chain 'a' and resid 82 through 86 removed outlier: 3.524A pdb=" N ASP a 85 " --> pdb=" O GLN a 82 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER a 86 " --> pdb=" O LEU a 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 82 through 86' Processing helix chain 'b' and resid 86 through 90 Processing helix chain 'b' and resid 135 through 139 Processing sheet with id=AA1, first strand: chain 'a' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'a' and resid 11 through 14 removed outlier: 3.695A pdb=" N ILE a 49 " --> pdb=" O TRP a 36 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS a 38 " --> pdb=" O PHE a 47 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE a 47 " --> pdb=" O LYS a 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 11 through 14 Processing sheet with id=AA4, first strand: chain 'a' and resid 19 through 21 removed outlier: 3.826A pdb=" N ALA a 75 " --> pdb=" O ASN a 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR a 63 " --> pdb=" O SER a 60 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 137 through 140 removed outlier: 3.752A pdb=" N THR a 168 " --> pdb=" O LYS a 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 152 through 152 removed outlier: 3.669A pdb=" N LYS a 181 " --> pdb=" O SER a 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 10 through 14 removed outlier: 5.084A pdb=" N TRP b 98 " --> pdb=" O TYR b 32 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N TYR b 32 " --> pdb=" O TRP b 98 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU b 48 " --> pdb=" O TRP b 35 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU b 37 " --> pdb=" O ARG b 46 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG b 46 " --> pdb=" O LEU b 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR b 49 " --> pdb=" O VAL b 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 10 through 14 Processing sheet with id=AA9, first strand: chain 'b' and resid 19 through 22 Processing sheet with id=AB1, first strand: chain 'b' and resid 125 through 129 removed outlier: 3.757A pdb=" N LEU b 145 " --> pdb=" O PHE b 129 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR b 144 " --> pdb=" O LEU b 189 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR b 183 " --> pdb=" O LYS b 150 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE b 186 " --> pdb=" O ASN b 175 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN b 175 " --> pdb=" O PHE b 186 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP b 188 " --> pdb=" O GLU b 173 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU b 173 " --> pdb=" O TRP b 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 157 through 162 1382 hydrogen bonds defined for protein. 4020 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: 3.60 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4151 1.33 - 1.45: 4494 1.45 - 1.57: 10921 1.57 - 1.69: 1 1.69 - 1.82: 180 Bond restraints: 19747 Sorted by residual: bond pdb=" C3C PUB B 201 " pdb=" C4C PUB B 201 " ideal model delta sigma weight residual 1.450 1.380 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C PUB H 201 " pdb=" C4C PUB H 201 " ideal model delta sigma weight residual 1.450 1.380 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C3C PUB D 201 " pdb=" C4C PUB D 201 " ideal model delta sigma weight residual 1.450 1.380 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C3C PUB F 201 " pdb=" C4C PUB F 201 " ideal model delta sigma weight residual 1.450 1.381 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3C PUB J 201 " pdb=" C4C PUB J 201 " ideal model delta sigma weight residual 1.450 1.381 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 19742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 25826 1.61 - 3.21: 863 3.21 - 4.82: 155 4.82 - 6.42: 46 6.42 - 8.03: 10 Bond angle restraints: 26900 Sorted by residual: angle pdb=" N THR B 145 " pdb=" CA THR B 145 " pdb=" C THR B 145 " ideal model delta sigma weight residual 113.72 107.61 6.11 1.30e+00 5.92e-01 2.21e+01 angle pdb=" C LYS a 17 " pdb=" N ALA a 18 " pdb=" CA ALA a 18 " ideal model delta sigma weight residual 122.99 117.17 5.82 1.41e+00 5.03e-01 1.70e+01 angle pdb=" CA VAL a 15 " pdb=" C VAL a 15 " pdb=" O VAL a 15 " ideal model delta sigma weight residual 122.13 118.08 4.05 1.11e+00 8.12e-01 1.33e+01 angle pdb=" CA ARG G 33 " pdb=" C ARG G 33 " pdb=" O ARG G 33 " ideal model delta sigma weight residual 121.00 117.23 3.77 1.05e+00 9.07e-01 1.29e+01 angle pdb=" N ASN D 35 " pdb=" CA ASN D 35 " pdb=" C ASN D 35 " ideal model delta sigma weight residual 111.71 115.65 -3.94 1.15e+00 7.56e-01 1.17e+01 ... (remaining 26895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11424 17.89 - 35.77: 1079 35.77 - 53.66: 228 53.66 - 71.55: 67 71.55 - 89.43: 28 Dihedral angle restraints: 12826 sinusoidal: 5796 harmonic: 7030 Sorted by residual: dihedral pdb=" CD ARG a 16 " pdb=" NE ARG a 16 " pdb=" CZ ARG a 16 " pdb=" NH1 ARG a 16 " ideal model delta sinusoidal sigma weight residual 0.00 89.43 -89.43 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS a 23 " pdb=" SG CYS a 23 " pdb=" SG CYS a 91 " pdb=" CB CYS a 91 " ideal model delta sinusoidal sigma weight residual 93.00 35.64 57.36 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CD ARG E 142 " pdb=" NE ARG E 142 " pdb=" CZ ARG E 142 " pdb=" NH1 ARG E 142 " ideal model delta sinusoidal sigma weight residual 0.00 -39.84 39.84 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 12823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2450 0.054 - 0.108: 439 0.108 - 0.161: 40 0.161 - 0.215: 18 0.215 - 0.269: 4 Chirality restraints: 2951 Sorted by residual: chirality pdb=" C1D PEB D 203 " pdb=" ND PEB D 203 " pdb=" C2D PEB D 203 " pdb=" CHC PEB D 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.83 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASN D 35 " pdb=" N ASN D 35 " pdb=" C ASN D 35 " pdb=" CB ASN D 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL a 74 " pdb=" CA VAL a 74 " pdb=" CG1 VAL a 74 " pdb=" CG2 VAL a 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2948 not shown) Planarity restraints: 3418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PEB D 203 " -0.314 2.00e-02 2.50e+03 3.81e-01 3.27e+03 pdb=" C1B PEB D 203 " 0.043 2.00e-02 2.50e+03 pdb=" C2B PEB D 203 " -0.151 2.00e-02 2.50e+03 pdb=" C3B PEB D 203 " 0.124 2.00e-02 2.50e+03 pdb=" C4B PEB D 203 " -0.127 2.00e-02 2.50e+03 pdb=" CAB PEB D 203 " 0.607 2.00e-02 2.50e+03 pdb=" CHA PEB D 203 " 0.618 2.00e-02 2.50e+03 pdb=" CHB PEB D 203 " -0.193 2.00e-02 2.50e+03 pdb=" CMB PEB D 203 " -0.605 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A PEB D 203 " -0.040 2.00e-02 2.50e+03 1.76e-01 3.86e+02 pdb=" C2A PEB D 203 " -0.079 2.00e-02 2.50e+03 pdb=" C4A PEB D 203 " 0.227 2.00e-02 2.50e+03 pdb=" NA PEB D 203 " -0.265 2.00e-02 2.50e+03 pdb=" OA PEB D 203 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A PUB B 201 " -0.037 2.00e-02 2.50e+03 1.22e-01 1.86e+02 pdb=" C2A PUB B 201 " -0.054 2.00e-02 2.50e+03 pdb=" C4A PUB B 201 " 0.154 2.00e-02 2.50e+03 pdb=" NA PUB B 201 " -0.181 2.00e-02 2.50e+03 pdb=" OA PUB B 201 " 0.118 2.00e-02 2.50e+03 ... (remaining 3415 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 99 2.40 - 3.02: 11806 3.02 - 3.65: 34448 3.65 - 4.27: 50337 4.27 - 4.90: 82209 Nonbonded interactions: 178899 Sorted by model distance: nonbonded pdb=" NH2 ARG C 142 " pdb=" OD1 ASP C 143 " model vdw 1.774 3.120 nonbonded pdb=" NZ LYS C 43 " pdb=" C4D PEB C 202 " model vdw 2.113 2.672 nonbonded pdb=" OD1 ASP H 13 " pdb=" OH TYR L 74 " model vdw 2.184 3.040 nonbonded pdb=" O ASP b 181 " pdb=" OD1 ASP b 181 " model vdw 2.191 3.040 nonbonded pdb=" O TYR H 74 " pdb=" OG1 THR H 75 " model vdw 2.199 3.040 ... (remaining 178894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 202) selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 202) selection = (chain 'F' and resid 1 through 202) selection = (chain 'H' and resid 1 through 202) selection = chain 'J' selection = (chain 'L' and resid 1 through 202) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.440 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19782 Z= 0.239 Angle : 0.704 8.031 26904 Z= 0.372 Chirality : 0.042 0.269 2951 Planarity : 0.014 0.493 3418 Dihedral : 15.065 89.435 8296 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.44 % Favored : 97.23 % Rotamer: Outliers : 0.99 % Allowed : 11.80 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.48 (0.17), residues: 2381 helix: 1.82 (0.12), residues: 1632 sheet: -1.09 (0.37), residues: 168 loop : -0.74 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 33 TYR 0.025 0.002 TYR L 74 PHE 0.023 0.002 PHE a 152 TRP 0.046 0.002 TRP b 76 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00425 (19747) covalent geometry : angle 0.70442 (26900) SS BOND : bond 0.00067 ( 2) SS BOND : angle 1.01657 ( 4) hydrogen bonds : bond 0.11449 ( 1368) hydrogen bonds : angle 5.21514 ( 4020) Misc. bond : bond 0.01208 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 405 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7606 (mp0) REVERT: A 77 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: A 114 ARG cc_start: 0.8366 (ttp-170) cc_final: 0.7914 (ttt180) REVERT: A 118 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7463 (mtp85) REVERT: A 121 ASN cc_start: 0.8730 (t0) cc_final: 0.8524 (t0) REVERT: B 79 MET cc_start: 0.9020 (tpt) cc_final: 0.8752 (tpt) REVERT: B 115 GLU cc_start: 0.7515 (tt0) cc_final: 0.6990 (mp0) REVERT: C 77 GLU cc_start: 0.7521 (tt0) cc_final: 0.7125 (tp30) REVERT: E 1 MET cc_start: 0.7866 (tpp) cc_final: 0.7361 (mmp) REVERT: G 71 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7410 (mm-30) REVERT: G 76 GLN cc_start: 0.8277 (tp40) cc_final: 0.7899 (tp-100) REVERT: G 139 CYS cc_start: 0.7555 (t) cc_final: 0.7315 (t) REVERT: I 1 MET cc_start: 0.8242 (tpp) cc_final: 0.7764 (tpp) REVERT: J 170 ASP cc_start: 0.8503 (m-30) cc_final: 0.8174 (m-30) REVERT: K 1 MET cc_start: 0.8335 (tpp) cc_final: 0.7906 (tpp) REVERT: K 77 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: K 158 TYR cc_start: 0.9104 (t80) cc_final: 0.8874 (t80) REVERT: L 59 MET cc_start: 0.9050 (ttp) cc_final: 0.8609 (ttp) REVERT: L 115 GLU cc_start: 0.7564 (pt0) cc_final: 0.7290 (pt0) REVERT: a 100 TRP cc_start: 0.7475 (t60) cc_final: 0.7244 (t60) outliers start: 19 outliers final: 12 residues processed: 414 average time/residue: 0.8160 time to fit residues: 372.1592 Evaluate side-chains 387 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 373 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.0170 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 0.0370 overall best weight: 1.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 76 GLN D 148 GLN G 32 GLN G 48 HIS H 25 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN a 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143641 restraints weight = 23564.663| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.07 r_work: 0.3672 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19782 Z= 0.198 Angle : 0.652 8.227 26904 Z= 0.323 Chirality : 0.041 0.222 2951 Planarity : 0.004 0.046 3418 Dihedral : 10.416 89.878 4340 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.18 % Favored : 97.27 % Rotamer: Outliers : 2.14 % Allowed : 12.01 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.37 (0.16), residues: 2381 helix: 1.61 (0.12), residues: 1679 sheet: -0.96 (0.37), residues: 169 loop : -0.58 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.020 0.002 TYR L 74 PHE 0.015 0.002 PHE a 152 TRP 0.018 0.002 TRP a 109 HIS 0.005 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00422 (19747) covalent geometry : angle 0.65222 (26900) SS BOND : bond 0.00345 ( 2) SS BOND : angle 1.39108 ( 4) hydrogen bonds : bond 0.05068 ( 1368) hydrogen bonds : angle 4.82867 ( 4020) Misc. bond : bond 0.00456 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 401 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7671 (mp0) REVERT: A 114 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.7897 (ttm-80) REVERT: A 118 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7487 (mtp85) REVERT: B 115 GLU cc_start: 0.7486 (tt0) cc_final: 0.7038 (mp0) REVERT: C 25 GLU cc_start: 0.8401 (tt0) cc_final: 0.8077 (tt0) REVERT: C 77 GLU cc_start: 0.7641 (tt0) cc_final: 0.7229 (tp30) REVERT: D 164 GLU cc_start: 0.8889 (tt0) cc_final: 0.8536 (tt0) REVERT: G 71 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7419 (mm-30) REVERT: G 76 GLN cc_start: 0.8392 (tp40) cc_final: 0.8012 (tp-100) REVERT: H 74 TYR cc_start: 0.8168 (t80) cc_final: 0.7950 (t80) REVERT: I 1 MET cc_start: 0.8284 (tpp) cc_final: 0.7870 (tpp) REVERT: J 170 ASP cc_start: 0.8506 (m-30) cc_final: 0.8216 (m-30) REVERT: K 1 MET cc_start: 0.8464 (tpp) cc_final: 0.8027 (tpp) REVERT: K 77 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: L 59 MET cc_start: 0.9064 (ttp) cc_final: 0.8662 (ttp) REVERT: L 78 ARG cc_start: 0.8729 (mtt90) cc_final: 0.8513 (mtt90) REVERT: L 115 GLU cc_start: 0.7646 (pt0) cc_final: 0.7437 (pt0) REVERT: a 148 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6213 (pt) outliers start: 41 outliers final: 21 residues processed: 420 average time/residue: 0.7882 time to fit residues: 365.6772 Evaluate side-chains 394 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 371 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN D 148 GLN G 32 GLN K 76 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN a 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146248 restraints weight = 23557.074| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.08 r_work: 0.3701 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19782 Z= 0.160 Angle : 0.610 8.099 26904 Z= 0.302 Chirality : 0.039 0.198 2951 Planarity : 0.004 0.084 3418 Dihedral : 10.082 87.325 4332 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.55 % Allowed : 1.85 % Favored : 97.61 % Rotamer: Outliers : 2.19 % Allowed : 13.21 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.51 (0.16), residues: 2381 helix: 1.81 (0.12), residues: 1643 sheet: -0.93 (0.35), residues: 180 loop : -0.72 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 142 TYR 0.020 0.001 TYR L 74 PHE 0.011 0.002 PHE a 152 TRP 0.018 0.001 TRP a 109 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00335 (19747) covalent geometry : angle 0.61010 (26900) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.34038 ( 4) hydrogen bonds : bond 0.04581 ( 1368) hydrogen bonds : angle 4.66827 ( 4020) Misc. bond : bond 0.00387 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 400 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7614 (mp0) REVERT: A 77 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: A 114 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.7810 (ttm-80) REVERT: A 118 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7418 (mtp85) REVERT: A 136 ASP cc_start: 0.8587 (m-30) cc_final: 0.8375 (m-30) REVERT: B 79 MET cc_start: 0.9073 (tpt) cc_final: 0.8866 (tpt) REVERT: B 115 GLU cc_start: 0.7575 (tt0) cc_final: 0.7048 (mp0) REVERT: B 164 GLU cc_start: 0.8769 (tt0) cc_final: 0.8478 (tt0) REVERT: C 25 GLU cc_start: 0.8394 (tt0) cc_final: 0.8001 (tt0) REVERT: C 30 ASN cc_start: 0.8415 (t0) cc_final: 0.8162 (t0) REVERT: C 77 GLU cc_start: 0.7512 (tt0) cc_final: 0.7175 (tp30) REVERT: D 164 GLU cc_start: 0.8861 (tt0) cc_final: 0.8544 (tt0) REVERT: E 1 MET cc_start: 0.8015 (tpp) cc_final: 0.7510 (mmp) REVERT: F 1 MET cc_start: 0.8420 (ptm) cc_final: 0.8183 (ptp) REVERT: G 49 GLU cc_start: 0.6894 (pm20) cc_final: 0.6558 (mp0) REVERT: G 71 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7384 (mm-30) REVERT: I 1 MET cc_start: 0.8249 (tpp) cc_final: 0.7747 (tpp) REVERT: I 77 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: J 170 ASP cc_start: 0.8507 (m-30) cc_final: 0.8213 (m-30) REVERT: K 1 MET cc_start: 0.8413 (tpp) cc_final: 0.7978 (tpp) REVERT: L 59 MET cc_start: 0.9037 (ttp) cc_final: 0.8737 (ttp) REVERT: L 115 GLU cc_start: 0.7629 (pt0) cc_final: 0.7413 (pt0) REVERT: a 43 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7231 (mmtm) outliers start: 42 outliers final: 24 residues processed: 423 average time/residue: 0.7766 time to fit residues: 362.7905 Evaluate side-chains 400 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 373 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 43 LYS Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 184 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 221 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN D 148 GLN E 76 GLN H 25 GLN H 148 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN a 8 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146015 restraints weight = 23525.022| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.07 r_work: 0.3698 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19782 Z= 0.164 Angle : 0.611 8.326 26904 Z= 0.301 Chirality : 0.040 0.195 2951 Planarity : 0.005 0.160 3418 Dihedral : 9.969 78.915 4327 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.55 % Allowed : 1.89 % Favored : 97.56 % Rotamer: Outliers : 2.56 % Allowed : 13.11 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.58 (0.16), residues: 2381 helix: 1.87 (0.12), residues: 1637 sheet: -0.78 (0.36), residues: 177 loop : -0.73 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 142 TYR 0.026 0.001 TYR L 74 PHE 0.009 0.002 PHE G 152 TRP 0.018 0.001 TRP a 109 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00346 (19747) covalent geometry : angle 0.61107 (26900) SS BOND : bond 0.00248 ( 2) SS BOND : angle 1.30698 ( 4) hydrogen bonds : bond 0.04557 ( 1368) hydrogen bonds : angle 4.62787 ( 4020) Misc. bond : bond 0.00417 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 390 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7612 (mp0) REVERT: A 114 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.7869 (ttm-80) REVERT: A 118 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7421 (mtp85) REVERT: A 136 ASP cc_start: 0.8546 (m-30) cc_final: 0.8318 (m-30) REVERT: B 115 GLU cc_start: 0.7566 (tt0) cc_final: 0.7036 (mp0) REVERT: C 77 GLU cc_start: 0.7530 (tt0) cc_final: 0.7185 (tp30) REVERT: D 39 ASP cc_start: 0.8701 (m-30) cc_final: 0.8462 (m-30) REVERT: D 164 GLU cc_start: 0.8871 (tt0) cc_final: 0.8636 (tt0) REVERT: G 49 GLU cc_start: 0.6848 (pm20) cc_final: 0.6501 (mp0) REVERT: G 71 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7366 (mm-30) REVERT: I 1 MET cc_start: 0.8235 (tpp) cc_final: 0.7817 (tpp) REVERT: J 170 ASP cc_start: 0.8495 (m-30) cc_final: 0.8203 (m-30) REVERT: K 1 MET cc_start: 0.8441 (tpp) cc_final: 0.8017 (tpp) REVERT: K 77 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: L 59 MET cc_start: 0.9047 (ttp) cc_final: 0.8623 (ttp) REVERT: a 43 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7219 (mmtm) REVERT: b 20 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6670 (mt-10) outliers start: 49 outliers final: 30 residues processed: 418 average time/residue: 0.7117 time to fit residues: 329.3214 Evaluate side-chains 399 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 366 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 43 LYS Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 184 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 30 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN G 80 ASN H 25 GLN I 30 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN K 76 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142057 restraints weight = 23583.720| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.06 r_work: 0.3647 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19782 Z= 0.237 Angle : 0.690 8.973 26904 Z= 0.338 Chirality : 0.042 0.219 2951 Planarity : 0.005 0.100 3418 Dihedral : 10.279 73.993 4327 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.10 % Favored : 97.35 % Rotamer: Outliers : 2.56 % Allowed : 13.58 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.36 (0.16), residues: 2381 helix: 1.60 (0.12), residues: 1673 sheet: -0.81 (0.37), residues: 179 loop : -0.59 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 142 TYR 0.020 0.002 TYR L 74 PHE 0.013 0.002 PHE b 151 TRP 0.017 0.002 TRP a 109 HIS 0.006 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00510 (19747) covalent geometry : angle 0.68996 (26900) SS BOND : bond 0.00424 ( 2) SS BOND : angle 1.86091 ( 4) hydrogen bonds : bond 0.05138 ( 1368) hydrogen bonds : angle 4.82096 ( 4020) Misc. bond : bond 0.00597 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 380 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7658 (mp0) REVERT: A 77 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: A 114 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.7834 (ttm-80) REVERT: A 118 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7412 (mtp85) REVERT: B 115 GLU cc_start: 0.7491 (tt0) cc_final: 0.6996 (mp0) REVERT: C 77 GLU cc_start: 0.7680 (tt0) cc_final: 0.7230 (tp30) REVERT: D 36 LYS cc_start: 0.8809 (mttt) cc_final: 0.8503 (mttt) REVERT: D 164 GLU cc_start: 0.8859 (tt0) cc_final: 0.8628 (tt0) REVERT: E 1 MET cc_start: 0.8053 (tpp) cc_final: 0.7535 (mmp) REVERT: G 71 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7404 (mm-30) REVERT: I 1 MET cc_start: 0.8243 (tpp) cc_final: 0.7766 (tpp) REVERT: J 170 ASP cc_start: 0.8536 (m-30) cc_final: 0.8243 (m-30) REVERT: K 1 MET cc_start: 0.8453 (tpp) cc_final: 0.8055 (tpp) REVERT: K 77 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: L 59 MET cc_start: 0.9112 (ttp) cc_final: 0.8758 (ttp) REVERT: a 43 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7337 (mmtm) REVERT: b 215 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6263 (tt0) outliers start: 49 outliers final: 30 residues processed: 411 average time/residue: 0.7516 time to fit residues: 341.0531 Evaluate side-chains 391 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 43 LYS Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 215 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN G 32 GLN G 76 GLN H 25 GLN I 32 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN K 32 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145153 restraints weight = 23547.232| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.07 r_work: 0.3688 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19782 Z= 0.168 Angle : 0.623 8.151 26904 Z= 0.308 Chirality : 0.040 0.202 2951 Planarity : 0.004 0.052 3418 Dihedral : 10.081 77.268 4327 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.55 % Allowed : 1.76 % Favored : 97.69 % Rotamer: Outliers : 2.30 % Allowed : 14.26 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.52 (0.16), residues: 2381 helix: 1.81 (0.12), residues: 1631 sheet: -0.65 (0.36), residues: 174 loop : -0.73 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 142 TYR 0.022 0.001 TYR L 74 PHE 0.009 0.002 PHE C 152 TRP 0.018 0.001 TRP a 109 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00356 (19747) covalent geometry : angle 0.62249 (26900) SS BOND : bond 0.00287 ( 2) SS BOND : angle 1.41725 ( 4) hydrogen bonds : bond 0.04603 ( 1368) hydrogen bonds : angle 4.66908 ( 4020) Misc. bond : bond 0.00438 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 390 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7671 (mp0) REVERT: A 77 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: A 114 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.7809 (ttm-80) REVERT: A 118 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7384 (mtp85) REVERT: A 136 ASP cc_start: 0.8540 (m-30) cc_final: 0.8337 (m-30) REVERT: B 115 GLU cc_start: 0.7530 (tt0) cc_final: 0.7058 (mp0) REVERT: C 30 ASN cc_start: 0.8395 (t0) cc_final: 0.8174 (t0) REVERT: C 77 GLU cc_start: 0.7542 (tt0) cc_final: 0.7136 (tp30) REVERT: C 142 ARG cc_start: 0.8815 (ttt-90) cc_final: 0.8427 (ttt-90) REVERT: D 164 GLU cc_start: 0.8860 (tt0) cc_final: 0.8581 (tt0) REVERT: E 1 MET cc_start: 0.7995 (tpp) cc_final: 0.7524 (mmp) REVERT: G 49 GLU cc_start: 0.6926 (pm20) cc_final: 0.6579 (mp0) REVERT: G 71 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7321 (mm-30) REVERT: I 1 MET cc_start: 0.8262 (tpp) cc_final: 0.7813 (tpp) REVERT: J 170 ASP cc_start: 0.8490 (m-30) cc_final: 0.8203 (m-30) REVERT: K 1 MET cc_start: 0.8466 (tpp) cc_final: 0.8032 (tpp) REVERT: K 77 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: L 59 MET cc_start: 0.9034 (ttp) cc_final: 0.8754 (ttp) outliers start: 44 outliers final: 29 residues processed: 416 average time/residue: 0.7490 time to fit residues: 344.2238 Evaluate side-chains 398 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 367 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 202 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN G 76 GLN I 30 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN K 76 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145989 restraints weight = 23494.166| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.06 r_work: 0.3709 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19782 Z= 0.155 Angle : 0.612 8.154 26904 Z= 0.302 Chirality : 0.040 0.206 2951 Planarity : 0.004 0.050 3418 Dihedral : 10.009 78.472 4327 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.93 % Favored : 97.56 % Rotamer: Outliers : 2.19 % Allowed : 14.83 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.62 (0.16), residues: 2381 helix: 1.87 (0.12), residues: 1637 sheet: -0.60 (0.36), residues: 177 loop : -0.64 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.026 0.001 TYR L 74 PHE 0.013 0.002 PHE a 123 TRP 0.019 0.001 TRP a 109 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00326 (19747) covalent geometry : angle 0.61145 (26900) SS BOND : bond 0.00240 ( 2) SS BOND : angle 1.24715 ( 4) hydrogen bonds : bond 0.04416 ( 1368) hydrogen bonds : angle 4.58994 ( 4020) Misc. bond : bond 0.00417 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 391 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7607 (mp0) REVERT: A 77 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 114 ARG cc_start: 0.8342 (ttp-170) cc_final: 0.7794 (ttm-80) REVERT: A 118 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7337 (mtp85) REVERT: B 115 GLU cc_start: 0.7546 (tt0) cc_final: 0.7014 (mp0) REVERT: C 77 GLU cc_start: 0.7488 (tt0) cc_final: 0.7111 (tp30) REVERT: C 142 ARG cc_start: 0.8786 (ttt-90) cc_final: 0.8454 (ttt-90) REVERT: D 164 GLU cc_start: 0.8862 (tt0) cc_final: 0.8657 (tt0) REVERT: E 1 MET cc_start: 0.7940 (tpp) cc_final: 0.7481 (mmp) REVERT: G 49 GLU cc_start: 0.6867 (pm20) cc_final: 0.6530 (mp0) REVERT: G 71 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7282 (mm-30) REVERT: H 25 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: I 1 MET cc_start: 0.8235 (tpp) cc_final: 0.7797 (tpp) REVERT: J 170 ASP cc_start: 0.8456 (m-30) cc_final: 0.8167 (m-30) REVERT: K 1 MET cc_start: 0.8399 (tpp) cc_final: 0.8048 (tpp) REVERT: K 77 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: L 59 MET cc_start: 0.9021 (ttp) cc_final: 0.8738 (ttp) outliers start: 42 outliers final: 29 residues processed: 417 average time/residue: 0.7977 time to fit residues: 366.7811 Evaluate side-chains 396 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN G 76 GLN G 80 ASN H 25 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.157027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143137 restraints weight = 23639.944| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.07 r_work: 0.3657 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19782 Z= 0.223 Angle : 0.689 8.493 26904 Z= 0.338 Chirality : 0.042 0.219 2951 Planarity : 0.005 0.086 3418 Dihedral : 10.331 88.078 4326 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.55 % Allowed : 1.89 % Favored : 97.56 % Rotamer: Outliers : 2.14 % Allowed : 15.67 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.41 (0.16), residues: 2381 helix: 1.71 (0.12), residues: 1637 sheet: -0.74 (0.36), residues: 179 loop : -0.73 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.028 0.002 TYR L 74 PHE 0.012 0.002 PHE b 151 TRP 0.018 0.002 TRP a 109 HIS 0.006 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00480 (19747) covalent geometry : angle 0.68830 (26900) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.76237 ( 4) hydrogen bonds : bond 0.04994 ( 1368) hydrogen bonds : angle 4.77149 ( 4020) Misc. bond : bond 0.00560 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 371 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7655 (mp0) REVERT: A 114 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7832 (ttm-80) REVERT: A 118 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7401 (mtp85) REVERT: B 115 GLU cc_start: 0.7491 (tt0) cc_final: 0.7000 (mp0) REVERT: C 77 GLU cc_start: 0.7661 (tt0) cc_final: 0.7226 (tp30) REVERT: C 142 ARG cc_start: 0.8844 (ttt-90) cc_final: 0.8511 (ttt-90) REVERT: D 164 GLU cc_start: 0.8871 (tt0) cc_final: 0.8617 (tt0) REVERT: G 49 GLU cc_start: 0.6857 (pm20) cc_final: 0.6550 (mp0) REVERT: G 71 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7277 (mm-30) REVERT: G 114 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7088 (pmt170) REVERT: I 1 MET cc_start: 0.8271 (tpp) cc_final: 0.7792 (tpp) REVERT: J 170 ASP cc_start: 0.8521 (m-30) cc_final: 0.8229 (m-30) REVERT: K 1 MET cc_start: 0.8427 (tpp) cc_final: 0.8020 (tpp) REVERT: K 77 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: L 59 MET cc_start: 0.9104 (ttp) cc_final: 0.8758 (ttp) REVERT: a 43 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7356 (mmtm) REVERT: b 20 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6689 (mt-10) outliers start: 41 outliers final: 32 residues processed: 397 average time/residue: 0.7527 time to fit residues: 329.9723 Evaluate side-chains 389 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 354 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 43 LYS Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 184 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 113 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN G 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN K 32 GLN L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143202 restraints weight = 23522.897| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.07 r_work: 0.3677 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19782 Z= 0.189 Angle : 0.664 9.514 26904 Z= 0.326 Chirality : 0.041 0.208 2951 Planarity : 0.005 0.083 3418 Dihedral : 10.389 88.774 4326 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.02 % Favored : 97.44 % Rotamer: Outliers : 1.93 % Allowed : 16.50 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.43 (0.16), residues: 2381 helix: 1.73 (0.12), residues: 1637 sheet: -0.76 (0.36), residues: 179 loop : -0.71 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.027 0.002 TYR L 74 PHE 0.009 0.002 PHE b 151 TRP 0.017 0.001 TRP a 109 HIS 0.006 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00403 (19747) covalent geometry : angle 0.66358 (26900) SS BOND : bond 0.00326 ( 2) SS BOND : angle 1.59647 ( 4) hydrogen bonds : bond 0.04732 ( 1368) hydrogen bonds : angle 4.72179 ( 4020) Misc. bond : bond 0.00520 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 367 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7608 (mp0) REVERT: A 77 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: A 114 ARG cc_start: 0.8374 (ttp-170) cc_final: 0.7814 (ttm-80) REVERT: A 118 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7330 (mtp85) REVERT: B 115 GLU cc_start: 0.7510 (tt0) cc_final: 0.7034 (mp0) REVERT: C 77 GLU cc_start: 0.7651 (tt0) cc_final: 0.7211 (tp30) REVERT: C 142 ARG cc_start: 0.8847 (ttt-90) cc_final: 0.8541 (ttt-90) REVERT: D 164 GLU cc_start: 0.8864 (tt0) cc_final: 0.8621 (tt0) REVERT: E 1 MET cc_start: 0.7964 (tpp) cc_final: 0.7539 (mmp) REVERT: G 43 LYS cc_start: 0.8008 (tptp) cc_final: 0.7774 (tptm) REVERT: G 49 GLU cc_start: 0.6905 (pm20) cc_final: 0.6553 (mp0) REVERT: G 71 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7301 (mm-30) REVERT: I 1 MET cc_start: 0.8281 (tpp) cc_final: 0.7827 (tpp) REVERT: J 170 ASP cc_start: 0.8519 (m-30) cc_final: 0.8231 (m-30) REVERT: K 1 MET cc_start: 0.8478 (tpp) cc_final: 0.8086 (tpp) REVERT: K 77 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: L 59 MET cc_start: 0.9063 (ttp) cc_final: 0.8713 (ttp) REVERT: a 43 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7319 (mmtm) REVERT: b 20 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6591 (mt-10) outliers start: 37 outliers final: 29 residues processed: 388 average time/residue: 0.7719 time to fit residues: 330.7352 Evaluate side-chains 390 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 357 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 43 LYS Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 196 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN G 76 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN a 129 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146630 restraints weight = 23655.944| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.07 r_work: 0.3720 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19782 Z= 0.150 Angle : 0.617 8.140 26904 Z= 0.306 Chirality : 0.040 0.201 2951 Planarity : 0.004 0.066 3418 Dihedral : 10.104 88.041 4326 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.97 % Favored : 97.56 % Rotamer: Outliers : 1.78 % Allowed : 16.55 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.59 (0.16), residues: 2381 helix: 1.84 (0.12), residues: 1637 sheet: -0.63 (0.36), residues: 181 loop : -0.66 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.028 0.002 TYR L 74 PHE 0.009 0.002 PHE C 152 TRP 0.016 0.001 TRP a 109 HIS 0.006 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00315 (19747) covalent geometry : angle 0.61686 (26900) SS BOND : bond 0.00246 ( 2) SS BOND : angle 1.18480 ( 4) hydrogen bonds : bond 0.04366 ( 1368) hydrogen bonds : angle 4.59217 ( 4020) Misc. bond : bond 0.00376 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4762 Ramachandran restraints generated. 2381 Oldfield, 0 Emsley, 2381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 381 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7617 (mp0) REVERT: A 77 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: A 114 ARG cc_start: 0.8329 (ttp-170) cc_final: 0.7660 (ttm-80) REVERT: A 118 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7308 (mtp85) REVERT: A 136 ASP cc_start: 0.8413 (m-30) cc_final: 0.8142 (m-30) REVERT: B 115 GLU cc_start: 0.7585 (tt0) cc_final: 0.7041 (mp0) REVERT: C 77 GLU cc_start: 0.7460 (tt0) cc_final: 0.7090 (tp30) REVERT: C 142 ARG cc_start: 0.8791 (ttt-90) cc_final: 0.8529 (ttt-90) REVERT: D 164 GLU cc_start: 0.8894 (tt0) cc_final: 0.8694 (tt0) REVERT: G 43 LYS cc_start: 0.7987 (tptp) cc_final: 0.7773 (tptm) REVERT: G 49 GLU cc_start: 0.6859 (pm20) cc_final: 0.6483 (mp0) REVERT: G 71 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7304 (mm-30) REVERT: G 114 ARG cc_start: 0.7372 (ttm110) cc_final: 0.7156 (ttp-170) REVERT: I 1 MET cc_start: 0.8270 (tpp) cc_final: 0.7830 (tpp) REVERT: J 170 ASP cc_start: 0.8446 (m-30) cc_final: 0.8157 (m-30) REVERT: K 1 MET cc_start: 0.8392 (tpp) cc_final: 0.8065 (tpp) REVERT: L 59 MET cc_start: 0.8955 (ttp) cc_final: 0.8652 (ttp) REVERT: a 30 TRP cc_start: 0.7028 (m-90) cc_final: 0.6816 (m-90) outliers start: 34 outliers final: 29 residues processed: 403 average time/residue: 0.7972 time to fit residues: 354.7881 Evaluate side-chains 389 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 359 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain a residue 73 SER Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 200 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 112 VAL Chi-restraints excluded: chain b residue 146 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 182 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 76 GLN G 76 GLN G 80 ASN I 30 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN a 66 ASN a 129 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140230 restraints weight = 23604.625| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.06 r_work: 0.3640 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 19782 Z= 0.263 Angle : 0.742 9.801 26904 Z= 0.363 Chirality : 0.044 0.223 2951 Planarity : 0.005 0.093 3418 Dihedral : 10.460 84.687 4326 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.14 % Favored : 97.31 % Rotamer: Outliers : 1.83 % Allowed : 16.71 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.88 % 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: 1.25 (0.16), residues: 2381 helix: 1.51 (0.12), residues: 1673 sheet: -0.78 (0.36), residues: 186 loop : -0.61 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 33 TYR 0.031 0.002 TYR F 74 PHE 0.016 0.003 PHE a 123 TRP 0.018 0.002 TRP a 109 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00570 (19747) covalent geometry : angle 0.74149 (26900) SS BOND : bond 0.00369 ( 2) SS BOND : angle 2.04824 ( 4) hydrogen bonds : bond 0.05263 ( 1368) hydrogen bonds : angle 4.87092 ( 4020) Misc. bond : bond 0.00640 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10593.15 seconds wall clock time: 180 minutes 51.57 seconds (10851.57 seconds total)