Starting phenix.real_space_refine on Sat Aug 23 14:22:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bx5_16308/08_2025/8bx5_16308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bx5_16308/08_2025/8bx5_16308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bx5_16308/08_2025/8bx5_16308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bx5_16308/08_2025/8bx5_16308.map" model { file = "/net/cci-nas-00/data/ceres_data/8bx5_16308/08_2025/8bx5_16308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bx5_16308/08_2025/8bx5_16308.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.013 sd= 0.122 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 75 5.16 5 C 8303 2.51 5 N 2031 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12527 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2487 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "D" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2489 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.28 Number of scatterers: 12527 At special positions: 0 Unit cell: (92.6016, 91.1547, 125.88, 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 75 16.00 O 2118 8.00 N 2031 7.00 C 8303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 544.6 milliseconds Enol-peptide restraints added in 1.4 microseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 16 sheets defined 38.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 219 through 239 removed outlier: 3.530A pdb=" N TYR A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.643A pdb=" N LYS A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.811A pdb=" N MET A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 441 removed outlier: 4.008A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.935A pdb=" N SER B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.826A pdb=" N ARG B 144 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 removed outlier: 4.698A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.829A pdb=" N LYS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.793A pdb=" N MET B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 442 removed outlier: 3.806A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 219 through 238 removed outlier: 4.147A pdb=" N MET C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.784A pdb=" N LYS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 307 Processing helix chain 'C' and resid 416 through 443 removed outlier: 3.832A pdb=" N ILE C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR C 443 " --> pdb=" O MET C 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 219 through 239 removed outlier: 4.542A pdb=" N MET D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Proline residue: D 228 - end of helix Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.593A pdb=" N LYS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 416 through 441 removed outlier: 3.908A pdb=" N ILE D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.021A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 219 through 239 removed outlier: 5.137A pdb=" N MET E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix removed outlier: 3.526A pdb=" N MET E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.537A pdb=" N LYS E 247 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 307 Processing helix chain 'E' and resid 416 through 441 removed outlier: 3.839A pdb=" N ILE E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 137 removed outlier: 6.478A pdb=" N VAL A 59 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 53 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR A 61 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP A 65 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL A 47 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR A 67 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 45 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 69 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU A 43 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.651A pdb=" N GLY A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 194 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 209 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 211 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 137 removed outlier: 6.437A pdb=" N VAL B 59 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 53 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR B 61 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP B 65 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL B 47 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR B 67 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 45 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLU B 69 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU B 43 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 39 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 169 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 41 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.523A pdb=" N VAL B 119 " --> pdb=" O MET B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 137 removed outlier: 7.054A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 39 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL C 41 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 90 Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.754A pdb=" N GLY C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 209 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C 211 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 137 removed outlier: 6.458A pdb=" N ASN D 63 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL D 50 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N TRP D 65 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 48 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR D 67 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR D 46 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLU D 69 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N GLU D 44 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AB4, first strand: chain 'D' and resid 101 through 102 removed outlier: 6.030A pdb=" N TYR D 205 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D 196 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY D 207 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG D 194 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 209 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY D 211 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 180 " --> pdb=" O VAL D 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 137 removed outlier: 6.403A pdb=" N ASN E 63 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL E 50 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TRP E 65 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL E 48 " --> pdb=" O TRP E 65 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR E 67 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR E 46 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU E 69 " --> pdb=" O GLU E 44 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N GLU E 44 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AB7, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.704A pdb=" N GLY E 207 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG E 194 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE E 209 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY E 211 " --> pdb=" O VAL E 190 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1665 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: 1.90 Time building geometry restraints manager: 1.30 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: 3345 1.33 - 1.45: 2459 1.45 - 1.58: 6913 1.58 - 1.70: 0 1.70 - 1.82: 131 Bond restraints: 12848 Sorted by residual: bond pdb=" N VAL B 166 " pdb=" CA VAL B 166 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.23e-02 6.61e+03 1.45e+01 bond pdb=" N VAL A 168 " pdb=" CA VAL A 168 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.37e+01 bond pdb=" N VAL D 166 " pdb=" CA VAL D 166 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N VAL C 166 " pdb=" CA VAL C 166 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N VAL E 168 " pdb=" CA VAL E 168 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 ... (remaining 12843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16997 1.81 - 3.61: 480 3.61 - 5.42: 114 5.42 - 7.22: 32 7.22 - 9.03: 10 Bond angle restraints: 17633 Sorted by residual: angle pdb=" N VAL A 166 " pdb=" CA VAL A 166 " pdb=" CB VAL A 166 " ideal model delta sigma weight residual 112.45 104.38 8.07 1.12e+00 7.97e-01 5.20e+01 angle pdb=" N VAL E 166 " pdb=" CA VAL E 166 " pdb=" CB VAL E 166 " ideal model delta sigma weight residual 111.23 102.20 9.03 1.65e+00 3.67e-01 2.99e+01 angle pdb=" N VAL C 166 " pdb=" CA VAL C 166 " pdb=" CB VAL C 166 " ideal model delta sigma weight residual 112.44 105.48 6.96 1.68e+00 3.54e-01 1.72e+01 angle pdb=" C MET E 265 " pdb=" N MET E 266 " pdb=" CA MET E 266 " ideal model delta sigma weight residual 121.14 114.03 7.11 1.75e+00 3.27e-01 1.65e+01 angle pdb=" CA VAL C 166 " pdb=" CB VAL C 166 " pdb=" CG1 VAL C 166 " ideal model delta sigma weight residual 110.40 117.18 -6.78 1.70e+00 3.46e-01 1.59e+01 ... (remaining 17628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.44: 6906 19.44 - 38.88: 481 38.88 - 58.31: 88 58.31 - 77.75: 12 77.75 - 97.19: 14 Dihedral angle restraints: 7501 sinusoidal: 2656 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS B 138 " pdb=" SG CYS B 138 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 35.53 57.47 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual -86.00 -29.53 -56.47 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" N VAL E 166 " pdb=" C VAL E 166 " pdb=" CA VAL E 166 " pdb=" CB VAL E 166 " ideal model delta harmonic sigma weight residual 123.40 112.50 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2142 0.146 - 0.292: 17 0.292 - 0.438: 3 0.438 - 0.584: 2 0.584 - 0.730: 3 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB VAL C 166 " pdb=" CA VAL C 166 " pdb=" CG1 VAL C 166 " pdb=" CG2 VAL C 166 " both_signs ideal model delta sigma weight residual False -2.63 -1.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 167 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2164 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.330 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG D 501 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 501 " -0.313 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C7 NAG C 501 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 501 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 501 " 0.490 2.00e-02 2.50e+03 pdb=" O7 NAG C 501 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.295 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG E 501 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.440 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " -0.045 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1552 2.75 - 3.29: 13264 3.29 - 3.83: 21602 3.83 - 4.36: 23739 4.36 - 4.90: 39905 Nonbonded interactions: 100062 Sorted by model distance: nonbonded pdb=" OG1 THR E 123 " pdb=" NZ LYS E 125 " model vdw 2.218 3.120 nonbonded pdb=" O ILE C 242 " pdb=" NH1 ARG C 249 " model vdw 2.247 3.120 nonbonded pdb=" O HOH A 601 " pdb=" O HOH B 501 " model vdw 2.257 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OH TYR B 220 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN C 34 " pdb=" OG SER C 36 " model vdw 2.260 3.040 ... (remaining 100057 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 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 126 or (resid 127 and \ (name N or name CA or name C or name O or name CB )) or resid 128 through 304 o \ r (resid 305 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 06 through 422 or (resid 423 through 424 and (name N or name CA or name C or nam \ e O or name CB )) or resid 425 through 443)) selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 126 or (resid 127 and \ (name N or name CA or name C or name O or name CB )) or resid 128 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE )) or resid 271 through 306 or (resid 307 and (name N or nam \ e CA or name C or name O or name CB )) or resid 414 through 422 or (resid 423 th \ rough 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 443)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 126 or (resid 127 and (name N or n \ ame CA or name C or name O or name CB )) or resid 128 through 443)) selection = (chain 'D' and (resid 12 through 422 or (resid 423 through 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 through 443)) selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 126 or (resid 127 and (name N or n \ ame CA or name C or name O or name CB )) or resid 128 through 422 or (resid 423 \ through 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 443)) } 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 group one per residue 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.003 0.047 12857 Z= 0.186 Angle : 0.805 12.662 17655 Z= 0.413 Chirality : 0.059 0.730 2167 Planarity : 0.012 0.288 2122 Dihedral : 14.220 97.188 4356 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.63 % Allowed : 0.16 % Favored : 99.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.21), residues: 1610 helix: 1.11 (0.23), residues: 520 sheet: -0.58 (0.28), residues: 350 loop : -1.55 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.028 0.002 TYR E 252 PHE 0.035 0.002 PHE A 289 TRP 0.027 0.002 TRP D 159 HIS 0.004 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00347 (12848) covalent geometry : angle 0.78430 (17633) SS BOND : bond 0.00247 ( 5) SS BOND : angle 1.89906 ( 10) hydrogen bonds : bond 0.11792 ( 589) hydrogen bonds : angle 5.37505 ( 1665) link_NAG-ASN : bond 0.01897 ( 4) link_NAG-ASN : angle 6.84784 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 456 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8037 (mtpt) REVERT: A 128 TRP cc_start: 0.7447 (t60) cc_final: 0.6474 (t60) REVERT: A 161 HIS cc_start: 0.7680 (p90) cc_final: 0.7127 (p90) REVERT: A 173 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8101 (tp-100) REVERT: A 234 PHE cc_start: 0.8644 (t80) cc_final: 0.8367 (t80) REVERT: A 241 PHE cc_start: 0.8703 (m-80) cc_final: 0.8112 (m-10) REVERT: A 287 TYR cc_start: 0.8909 (t80) cc_final: 0.8454 (t80) REVERT: A 305 MET cc_start: 0.7784 (ppp) cc_final: 0.6773 (mmt) REVERT: B 29 ILE cc_start: 0.7954 (mt) cc_final: 0.7641 (mm) REVERT: B 85 LEU cc_start: 0.9053 (tp) cc_final: 0.8805 (pp) REVERT: B 127 MET cc_start: 0.6870 (mmt) cc_final: 0.5778 (tpt) REVERT: B 227 MET cc_start: 0.8115 (ttm) cc_final: 0.7109 (tpp) REVERT: B 256 LEU cc_start: 0.9370 (mm) cc_final: 0.9169 (mm) REVERT: B 287 TYR cc_start: 0.8743 (t80) cc_final: 0.8322 (t80) REVERT: B 301 MET cc_start: 0.8903 (mmp) cc_final: 0.8323 (ptm) REVERT: C 62 THR cc_start: 0.9011 (p) cc_final: 0.8792 (p) REVERT: C 151 MET cc_start: 0.7088 (ttp) cc_final: 0.6860 (ttm) REVERT: C 166 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8369 (m) REVERT: C 231 LEU cc_start: 0.8957 (mt) cc_final: 0.8570 (mt) REVERT: C 234 PHE cc_start: 0.9301 (t80) cc_final: 0.8747 (t80) REVERT: C 266 MET cc_start: 0.9012 (ptp) cc_final: 0.8640 (ptm) REVERT: C 269 ASP cc_start: 0.8311 (m-30) cc_final: 0.8048 (m-30) REVERT: C 287 TYR cc_start: 0.8846 (t80) cc_final: 0.8006 (t80) REVERT: C 301 MET cc_start: 0.9088 (mmp) cc_final: 0.8532 (ppp) REVERT: D 103 PHE cc_start: 0.8142 (m-80) cc_final: 0.7678 (m-80) REVERT: D 137 PHE cc_start: 0.8343 (m-10) cc_final: 0.8136 (m-80) REVERT: D 266 MET cc_start: 0.9129 (ptp) cc_final: 0.8761 (ptt) REVERT: D 287 TYR cc_start: 0.9180 (t80) cc_final: 0.8760 (t80) REVERT: D 425 PHE cc_start: 0.8368 (t80) cc_final: 0.7684 (t80) REVERT: D 435 ILE cc_start: 0.8971 (pt) cc_final: 0.8709 (tp) REVERT: E 62 THR cc_start: 0.8838 (p) cc_final: 0.8615 (p) REVERT: E 74 GLN cc_start: 0.8462 (mp10) cc_final: 0.8249 (mp10) REVERT: E 102 LEU cc_start: 0.9159 (tp) cc_final: 0.8550 (tp) REVERT: E 225 PHE cc_start: 0.8512 (m-80) cc_final: 0.8054 (m-80) REVERT: E 235 LEU cc_start: 0.9434 (mt) cc_final: 0.8798 (tp) REVERT: E 238 LEU cc_start: 0.9094 (mp) cc_final: 0.8762 (mp) REVERT: E 268 SER cc_start: 0.9173 (p) cc_final: 0.8970 (p) REVERT: E 291 MET cc_start: 0.9072 (tpp) cc_final: 0.8482 (mmt) REVERT: E 428 PHE cc_start: 0.9458 (m-10) cc_final: 0.9147 (m-10) outliers start: 8 outliers final: 0 residues processed: 464 average time/residue: 0.0866 time to fit residues: 62.6148 Evaluate side-chains 378 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS C 196 GLN D 161 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083172 restraints weight = 37468.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.085741 restraints weight = 24896.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087559 restraints weight = 18519.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088906 restraints weight = 14920.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089812 restraints weight = 12681.284| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12857 Z= 0.167 Angle : 0.693 12.781 17655 Z= 0.338 Chirality : 0.047 0.365 2167 Planarity : 0.004 0.039 2122 Dihedral : 6.713 50.709 1855 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.21), residues: 1610 helix: 1.32 (0.23), residues: 525 sheet: -1.10 (0.26), residues: 420 loop : -1.33 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 133 TYR 0.027 0.001 TYR D 252 PHE 0.031 0.002 PHE C 428 TRP 0.012 0.001 TRP D 159 HIS 0.009 0.001 HIS D 131 Details of bonding type rmsd covalent geometry : bond 0.00362 (12848) covalent geometry : angle 0.68639 (17633) SS BOND : bond 0.00136 ( 5) SS BOND : angle 1.94650 ( 10) hydrogen bonds : bond 0.04101 ( 589) hydrogen bonds : angle 4.80925 ( 1665) link_NAG-ASN : bond 0.01156 ( 4) link_NAG-ASN : angle 3.40607 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 416 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8131 (tttm) REVERT: A 128 TRP cc_start: 0.7814 (t60) cc_final: 0.6721 (t60) REVERT: A 161 HIS cc_start: 0.7810 (p-80) cc_final: 0.7205 (p-80) REVERT: A 173 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8055 (tp-100) REVERT: A 234 PHE cc_start: 0.8748 (t80) cc_final: 0.8474 (t80) REVERT: A 271 MET cc_start: 0.8786 (tmm) cc_final: 0.8536 (tmm) REVERT: A 287 TYR cc_start: 0.8516 (t80) cc_final: 0.8220 (t80) REVERT: A 296 LEU cc_start: 0.9067 (mt) cc_final: 0.8831 (mt) REVERT: A 425 PHE cc_start: 0.8522 (t80) cc_final: 0.8301 (t80) REVERT: B 85 LEU cc_start: 0.9021 (tp) cc_final: 0.8792 (pp) REVERT: B 125 LYS cc_start: 0.8390 (tttp) cc_final: 0.8153 (tttm) REVERT: B 213 LYS cc_start: 0.8823 (mmpt) cc_final: 0.8622 (mmmt) REVERT: B 266 MET cc_start: 0.9049 (ppp) cc_final: 0.8749 (ppp) REVERT: B 269 ASP cc_start: 0.7749 (m-30) cc_final: 0.7453 (m-30) REVERT: B 287 TYR cc_start: 0.8472 (t80) cc_final: 0.8267 (t80) REVERT: C 151 MET cc_start: 0.8317 (ttp) cc_final: 0.8068 (ttm) REVERT: C 231 LEU cc_start: 0.9009 (mt) cc_final: 0.8776 (mt) REVERT: C 266 MET cc_start: 0.9264 (ptp) cc_final: 0.9036 (ptm) REVERT: C 287 TYR cc_start: 0.8595 (t80) cc_final: 0.8203 (t80) REVERT: C 429 LEU cc_start: 0.8805 (mt) cc_final: 0.8556 (mt) REVERT: C 435 ILE cc_start: 0.8730 (pt) cc_final: 0.8378 (tp) REVERT: D 103 PHE cc_start: 0.8444 (m-80) cc_final: 0.7909 (m-80) REVERT: D 265 MET cc_start: 0.8470 (ttp) cc_final: 0.8208 (ttp) REVERT: D 266 MET cc_start: 0.9308 (ptp) cc_final: 0.9034 (ptt) REVERT: D 287 TYR cc_start: 0.8838 (t80) cc_final: 0.8484 (t80) REVERT: D 301 MET cc_start: 0.8168 (mmm) cc_final: 0.7737 (mmm) REVERT: D 425 PHE cc_start: 0.8329 (t80) cc_final: 0.8073 (t80) REVERT: E 62 THR cc_start: 0.9228 (p) cc_final: 0.8985 (p) REVERT: E 151 MET cc_start: 0.8642 (ttp) cc_final: 0.8371 (ttp) REVERT: E 215 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8150 (mmmm) REVERT: E 225 PHE cc_start: 0.8681 (m-80) cc_final: 0.8316 (m-80) REVERT: E 227 MET cc_start: 0.8305 (ttm) cc_final: 0.8022 (ttm) REVERT: E 235 LEU cc_start: 0.9521 (mt) cc_final: 0.9176 (mt) REVERT: E 238 LEU cc_start: 0.8884 (mp) cc_final: 0.8662 (mp) REVERT: E 287 TYR cc_start: 0.8599 (t80) cc_final: 0.8366 (t80) REVERT: E 301 MET cc_start: 0.7387 (mmm) cc_final: 0.6849 (mmm) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.0758 time to fit residues: 49.5970 Evaluate side-chains 379 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083076 restraints weight = 37212.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085653 restraints weight = 24575.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.087504 restraints weight = 18243.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088782 restraints weight = 14653.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.089519 restraints weight = 12553.797| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12857 Z= 0.155 Angle : 0.673 10.837 17655 Z= 0.333 Chirality : 0.046 0.274 2167 Planarity : 0.003 0.030 2122 Dihedral : 6.003 56.672 1855 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.21), residues: 1610 helix: 1.31 (0.22), residues: 525 sheet: -1.00 (0.26), residues: 425 loop : -1.30 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.020 0.001 TYR B 223 PHE 0.031 0.002 PHE D 289 TRP 0.017 0.001 TRP B 185 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00344 (12848) covalent geometry : angle 0.66797 (17633) SS BOND : bond 0.00379 ( 5) SS BOND : angle 2.29232 ( 10) hydrogen bonds : bond 0.03986 ( 589) hydrogen bonds : angle 4.75997 ( 1665) link_NAG-ASN : bond 0.00621 ( 4) link_NAG-ASN : angle 2.50989 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 0.491 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 21 ILE cc_start: 0.9566 (tp) cc_final: 0.9345 (mm) REVERT: A 173 GLN cc_start: 0.8286 (tp-100) cc_final: 0.7992 (tp-100) REVERT: A 215 LYS cc_start: 0.8282 (mmmt) cc_final: 0.8064 (mmmt) REVERT: A 234 PHE cc_start: 0.8914 (t80) cc_final: 0.8674 (t80) REVERT: A 241 PHE cc_start: 0.8577 (m-80) cc_final: 0.8324 (m-10) REVERT: A 265 MET cc_start: 0.8503 (ttt) cc_final: 0.8073 (ttm) REVERT: A 287 TYR cc_start: 0.8484 (t80) cc_final: 0.7964 (t80) REVERT: A 296 LEU cc_start: 0.9068 (mt) cc_final: 0.8748 (mt) REVERT: A 425 PHE cc_start: 0.8614 (t80) cc_final: 0.8409 (t80) REVERT: B 72 ASP cc_start: 0.8681 (t70) cc_final: 0.8312 (t0) REVERT: B 85 LEU cc_start: 0.9005 (tp) cc_final: 0.8671 (pp) REVERT: B 103 PHE cc_start: 0.9033 (m-80) cc_final: 0.8634 (m-80) REVERT: B 266 MET cc_start: 0.9015 (ppp) cc_final: 0.8580 (ppp) REVERT: B 268 SER cc_start: 0.9263 (p) cc_final: 0.8972 (t) REVERT: B 269 ASP cc_start: 0.7588 (m-30) cc_final: 0.7379 (m-30) REVERT: B 287 TYR cc_start: 0.8509 (t80) cc_final: 0.8167 (t80) REVERT: B 298 PHE cc_start: 0.9259 (m-10) cc_final: 0.8171 (m-10) REVERT: B 429 LEU cc_start: 0.9050 (pp) cc_final: 0.8791 (pp) REVERT: C 151 MET cc_start: 0.8447 (ttp) cc_final: 0.8129 (ttm) REVERT: C 231 LEU cc_start: 0.9076 (mt) cc_final: 0.8875 (mt) REVERT: C 266 MET cc_start: 0.9257 (ptp) cc_final: 0.8966 (ptm) REVERT: C 269 ASP cc_start: 0.8328 (m-30) cc_final: 0.8117 (m-30) REVERT: C 287 TYR cc_start: 0.8624 (t80) cc_final: 0.8177 (t80) REVERT: C 429 LEU cc_start: 0.8817 (mt) cc_final: 0.8532 (mt) REVERT: C 435 ILE cc_start: 0.8681 (pt) cc_final: 0.8338 (tp) REVERT: D 102 LEU cc_start: 0.9264 (tt) cc_final: 0.8962 (tt) REVERT: D 103 PHE cc_start: 0.8594 (m-80) cc_final: 0.7924 (m-80) REVERT: D 252 TYR cc_start: 0.8846 (t80) cc_final: 0.8589 (t80) REVERT: D 287 TYR cc_start: 0.8820 (t80) cc_final: 0.8414 (t80) REVERT: D 289 PHE cc_start: 0.9113 (t80) cc_final: 0.8757 (t80) REVERT: D 425 PHE cc_start: 0.8411 (t80) cc_final: 0.8127 (t80) REVERT: D 429 LEU cc_start: 0.9120 (mt) cc_final: 0.8904 (mt) REVERT: E 62 THR cc_start: 0.9271 (p) cc_final: 0.8819 (t) REVERT: E 151 MET cc_start: 0.8560 (ttp) cc_final: 0.8327 (ttp) REVERT: E 196 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8773 (tp40) REVERT: E 215 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8277 (mmmm) REVERT: E 225 PHE cc_start: 0.8649 (m-80) cc_final: 0.8204 (m-80) REVERT: E 235 LEU cc_start: 0.9412 (mt) cc_final: 0.8981 (mm) REVERT: E 238 LEU cc_start: 0.8815 (mp) cc_final: 0.8592 (mp) REVERT: E 252 TYR cc_start: 0.8903 (t80) cc_final: 0.8500 (t80) REVERT: E 291 MET cc_start: 0.9137 (mmt) cc_final: 0.8853 (mmt) outliers start: 1 outliers final: 0 residues processed: 429 average time/residue: 0.0838 time to fit residues: 57.5828 Evaluate side-chains 371 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.104673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083219 restraints weight = 37192.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085754 restraints weight = 24766.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.087613 restraints weight = 18499.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088944 restraints weight = 14902.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.089879 restraints weight = 12687.864| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12857 Z= 0.144 Angle : 0.660 9.521 17655 Z= 0.328 Chirality : 0.045 0.248 2167 Planarity : 0.003 0.030 2122 Dihedral : 5.560 54.338 1855 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.21), residues: 1610 helix: 1.28 (0.22), residues: 525 sheet: -0.80 (0.26), residues: 400 loop : -1.24 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 249 TYR 0.024 0.002 TYR B 223 PHE 0.024 0.002 PHE A 428 TRP 0.028 0.001 TRP C 65 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00318 (12848) covalent geometry : angle 0.65527 (17633) SS BOND : bond 0.00258 ( 5) SS BOND : angle 2.03179 ( 10) hydrogen bonds : bond 0.03860 ( 589) hydrogen bonds : angle 4.65847 ( 1665) link_NAG-ASN : bond 0.00725 ( 4) link_NAG-ASN : angle 2.44375 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 425 time to evaluate : 0.516 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 125 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8295 (ttpp) REVERT: A 173 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7946 (tp-100) REVERT: A 215 LYS cc_start: 0.8343 (mmmt) cc_final: 0.7926 (mmmt) REVERT: A 234 PHE cc_start: 0.8909 (t80) cc_final: 0.8663 (t80) REVERT: A 265 MET cc_start: 0.8506 (ttt) cc_final: 0.8138 (ttm) REVERT: A 287 TYR cc_start: 0.8402 (t80) cc_final: 0.7965 (t80) REVERT: A 296 LEU cc_start: 0.9046 (mt) cc_final: 0.8729 (mt) REVERT: A 425 PHE cc_start: 0.8638 (t80) cc_final: 0.8346 (t80) REVERT: B 72 ASP cc_start: 0.8701 (t70) cc_final: 0.8356 (t0) REVERT: B 103 PHE cc_start: 0.9057 (m-80) cc_final: 0.8804 (m-80) REVERT: B 266 MET cc_start: 0.8992 (ppp) cc_final: 0.8544 (ppp) REVERT: B 268 SER cc_start: 0.9227 (p) cc_final: 0.8949 (t) REVERT: B 269 ASP cc_start: 0.7580 (m-30) cc_final: 0.7312 (m-30) REVERT: B 287 TYR cc_start: 0.8586 (t80) cc_final: 0.8037 (t80) REVERT: C 65 TRP cc_start: 0.9301 (p90) cc_final: 0.8955 (p90) REVERT: C 151 MET cc_start: 0.8398 (ttp) cc_final: 0.8168 (ttp) REVERT: C 187 VAL cc_start: 0.9562 (t) cc_final: 0.9183 (t) REVERT: C 287 TYR cc_start: 0.8626 (t80) cc_final: 0.8187 (t80) REVERT: C 429 LEU cc_start: 0.8844 (mt) cc_final: 0.8600 (mt) REVERT: C 435 ILE cc_start: 0.8728 (pt) cc_final: 0.8356 (tp) REVERT: D 103 PHE cc_start: 0.8596 (m-80) cc_final: 0.7978 (m-80) REVERT: D 287 TYR cc_start: 0.8787 (t80) cc_final: 0.8398 (t80) REVERT: D 289 PHE cc_start: 0.9188 (t80) cc_final: 0.8647 (t80) REVERT: D 425 PHE cc_start: 0.8434 (t80) cc_final: 0.8132 (t80) REVERT: D 429 LEU cc_start: 0.9115 (mt) cc_final: 0.8910 (mt) REVERT: E 62 THR cc_start: 0.9170 (p) cc_final: 0.8943 (p) REVERT: E 151 MET cc_start: 0.8384 (ttp) cc_final: 0.8088 (ttp) REVERT: E 196 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8733 (tp40) REVERT: E 215 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8163 (mmmm) REVERT: E 225 PHE cc_start: 0.8563 (m-80) cc_final: 0.8159 (m-80) REVERT: E 235 LEU cc_start: 0.9482 (mt) cc_final: 0.8975 (mm) REVERT: E 238 LEU cc_start: 0.8797 (mp) cc_final: 0.8518 (mp) REVERT: E 252 TYR cc_start: 0.8925 (t80) cc_final: 0.8367 (t80) REVERT: E 287 TYR cc_start: 0.8637 (t80) cc_final: 0.8402 (t80) REVERT: E 291 MET cc_start: 0.9141 (mmt) cc_final: 0.8739 (mmt) REVERT: E 296 LEU cc_start: 0.9300 (mt) cc_final: 0.9072 (mt) outliers start: 2 outliers final: 0 residues processed: 426 average time/residue: 0.0817 time to fit residues: 55.7983 Evaluate side-chains 362 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 177 GLN B 277 ASN E 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.104528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083020 restraints weight = 37013.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085601 restraints weight = 24599.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.087456 restraints weight = 18310.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088805 restraints weight = 14746.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.089805 restraints weight = 12542.048| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12857 Z= 0.130 Angle : 0.672 10.728 17655 Z= 0.327 Chirality : 0.046 0.228 2167 Planarity : 0.003 0.029 2122 Dihedral : 5.346 53.978 1855 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 0.16 % Allowed : 4.37 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.21), residues: 1610 helix: 1.33 (0.22), residues: 525 sheet: -0.90 (0.26), residues: 410 loop : -1.23 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 249 TYR 0.018 0.001 TYR B 223 PHE 0.026 0.002 PHE D 289 TRP 0.031 0.001 TRP D 65 HIS 0.006 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00291 (12848) covalent geometry : angle 0.66740 (17633) SS BOND : bond 0.00481 ( 5) SS BOND : angle 2.12653 ( 10) hydrogen bonds : bond 0.03788 ( 589) hydrogen bonds : angle 4.64366 ( 1665) link_NAG-ASN : bond 0.00644 ( 4) link_NAG-ASN : angle 2.31870 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 0.543 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 125 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8309 (ttpp) REVERT: A 173 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7926 (tp-100) REVERT: A 234 PHE cc_start: 0.8900 (t80) cc_final: 0.8657 (t80) REVERT: A 241 PHE cc_start: 0.8546 (m-80) cc_final: 0.8268 (m-10) REVERT: A 265 MET cc_start: 0.8480 (ttt) cc_final: 0.8056 (ttm) REVERT: A 266 MET cc_start: 0.9305 (ptp) cc_final: 0.9078 (ptp) REVERT: A 287 TYR cc_start: 0.8368 (t80) cc_final: 0.7870 (t80) REVERT: A 296 LEU cc_start: 0.9039 (mt) cc_final: 0.8714 (mt) REVERT: A 425 PHE cc_start: 0.8658 (t80) cc_final: 0.8357 (t80) REVERT: B 72 ASP cc_start: 0.8678 (t70) cc_final: 0.8361 (t0) REVERT: B 227 MET cc_start: 0.8478 (ttm) cc_final: 0.8019 (tpp) REVERT: B 266 MET cc_start: 0.8979 (ppp) cc_final: 0.8599 (ppp) REVERT: B 268 SER cc_start: 0.9290 (p) cc_final: 0.9034 (t) REVERT: B 269 ASP cc_start: 0.7600 (m-30) cc_final: 0.7354 (m-30) REVERT: B 287 TYR cc_start: 0.8519 (t80) cc_final: 0.7959 (t80) REVERT: C 65 TRP cc_start: 0.9333 (p90) cc_final: 0.9077 (p90) REVERT: C 151 MET cc_start: 0.8442 (ttp) cc_final: 0.8174 (ttp) REVERT: C 256 LEU cc_start: 0.8933 (mm) cc_final: 0.8713 (mm) REVERT: C 287 TYR cc_start: 0.8555 (t80) cc_final: 0.8134 (t80) REVERT: C 301 MET cc_start: 0.8128 (mmm) cc_final: 0.7758 (mmm) REVERT: C 429 LEU cc_start: 0.8929 (mt) cc_final: 0.8623 (mt) REVERT: C 435 ILE cc_start: 0.8699 (pt) cc_final: 0.8377 (tp) REVERT: D 65 TRP cc_start: 0.9304 (p90) cc_final: 0.9076 (p90) REVERT: D 103 PHE cc_start: 0.8486 (m-80) cc_final: 0.7914 (m-80) REVERT: D 266 MET cc_start: 0.9230 (ptp) cc_final: 0.9030 (ptp) REVERT: D 287 TYR cc_start: 0.8717 (t80) cc_final: 0.8347 (t80) REVERT: D 425 PHE cc_start: 0.8370 (t80) cc_final: 0.8049 (t80) REVERT: D 429 LEU cc_start: 0.9122 (mt) cc_final: 0.8882 (mt) REVERT: E 151 MET cc_start: 0.8460 (ttp) cc_final: 0.8105 (ttp) REVERT: E 196 GLN cc_start: 0.9070 (tp40) cc_final: 0.8689 (tp40) REVERT: E 215 LYS cc_start: 0.8438 (mmmm) cc_final: 0.8138 (mmmm) REVERT: E 225 PHE cc_start: 0.8563 (m-80) cc_final: 0.8203 (m-80) REVERT: E 227 MET cc_start: 0.8287 (ttm) cc_final: 0.8023 (ttm) REVERT: E 235 LEU cc_start: 0.9403 (mt) cc_final: 0.8852 (mm) REVERT: E 238 LEU cc_start: 0.8992 (mp) cc_final: 0.8776 (mp) REVERT: E 252 TYR cc_start: 0.8909 (t80) cc_final: 0.8359 (t80) REVERT: E 256 LEU cc_start: 0.8915 (mm) cc_final: 0.8662 (mm) REVERT: E 291 MET cc_start: 0.9087 (mmt) cc_final: 0.8633 (mmt) outliers start: 2 outliers final: 0 residues processed: 424 average time/residue: 0.0820 time to fit residues: 55.3610 Evaluate side-chains 359 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082890 restraints weight = 36589.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085422 restraints weight = 24410.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087245 restraints weight = 18209.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088607 restraints weight = 14661.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089498 restraints weight = 12445.953| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12857 Z= 0.143 Angle : 0.665 14.032 17655 Z= 0.329 Chirality : 0.045 0.215 2167 Planarity : 0.003 0.029 2122 Dihedral : 5.237 54.065 1855 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.21), residues: 1610 helix: 1.37 (0.22), residues: 525 sheet: -0.84 (0.26), residues: 410 loop : -1.22 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 249 TYR 0.032 0.001 TYR D 252 PHE 0.025 0.002 PHE D 289 TRP 0.018 0.001 TRP D 65 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00322 (12848) covalent geometry : angle 0.66094 (17633) SS BOND : bond 0.00191 ( 5) SS BOND : angle 2.00782 ( 10) hydrogen bonds : bond 0.03844 ( 589) hydrogen bonds : angle 4.55695 ( 1665) link_NAG-ASN : bond 0.00600 ( 4) link_NAG-ASN : angle 2.25505 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9467 (tp) cc_final: 0.9242 (mm) REVERT: A 103 PHE cc_start: 0.9168 (m-10) cc_final: 0.8888 (m-80) REVERT: A 125 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8382 (tttt) REVERT: A 128 TRP cc_start: 0.7977 (t60) cc_final: 0.7626 (t60) REVERT: A 173 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7894 (tp-100) REVERT: A 234 PHE cc_start: 0.8900 (t80) cc_final: 0.8668 (t80) REVERT: A 241 PHE cc_start: 0.8582 (m-80) cc_final: 0.8284 (m-10) REVERT: A 265 MET cc_start: 0.8490 (ttt) cc_final: 0.8115 (ttm) REVERT: A 287 TYR cc_start: 0.8331 (t80) cc_final: 0.7883 (t80) REVERT: A 296 LEU cc_start: 0.9077 (mt) cc_final: 0.8718 (mt) REVERT: A 425 PHE cc_start: 0.8625 (t80) cc_final: 0.8351 (t80) REVERT: B 72 ASP cc_start: 0.8687 (t70) cc_final: 0.8484 (t0) REVERT: B 127 MET cc_start: 0.6757 (tpt) cc_final: 0.6508 (tpt) REVERT: B 225 PHE cc_start: 0.8444 (m-80) cc_final: 0.8028 (m-80) REVERT: B 266 MET cc_start: 0.8947 (ppp) cc_final: 0.8526 (ppp) REVERT: B 269 ASP cc_start: 0.7620 (m-30) cc_final: 0.7380 (m-30) REVERT: B 287 TYR cc_start: 0.8365 (t80) cc_final: 0.8160 (t80) REVERT: C 65 TRP cc_start: 0.9382 (p90) cc_final: 0.9095 (p90) REVERT: C 287 TYR cc_start: 0.8608 (t80) cc_final: 0.8190 (t80) REVERT: C 429 LEU cc_start: 0.9012 (mt) cc_final: 0.8675 (mt) REVERT: C 435 ILE cc_start: 0.8748 (pt) cc_final: 0.8417 (tp) REVERT: D 103 PHE cc_start: 0.8525 (m-80) cc_final: 0.7909 (m-80) REVERT: D 137 PHE cc_start: 0.8640 (m-80) cc_final: 0.8274 (m-80) REVERT: D 155 VAL cc_start: 0.9109 (p) cc_final: 0.8891 (p) REVERT: D 266 MET cc_start: 0.9240 (ptp) cc_final: 0.8945 (ptt) REVERT: D 287 TYR cc_start: 0.8751 (t80) cc_final: 0.8353 (t80) REVERT: D 425 PHE cc_start: 0.8546 (t80) cc_final: 0.8247 (t80) REVERT: D 429 LEU cc_start: 0.9137 (mt) cc_final: 0.8904 (mt) REVERT: E 62 THR cc_start: 0.9202 (p) cc_final: 0.8979 (p) REVERT: E 125 LYS cc_start: 0.6425 (tptt) cc_final: 0.6108 (tptp) REVERT: E 151 MET cc_start: 0.8452 (ttp) cc_final: 0.8178 (ttp) REVERT: E 196 GLN cc_start: 0.9103 (tp40) cc_final: 0.8766 (tp40) REVERT: E 215 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8186 (mmmm) REVERT: E 225 PHE cc_start: 0.8552 (m-80) cc_final: 0.8198 (m-80) REVERT: E 227 MET cc_start: 0.8259 (ttm) cc_final: 0.8003 (ttm) REVERT: E 235 LEU cc_start: 0.9424 (mt) cc_final: 0.8993 (mt) REVERT: E 238 LEU cc_start: 0.8984 (mp) cc_final: 0.8775 (mp) REVERT: E 252 TYR cc_start: 0.8888 (t80) cc_final: 0.8369 (t80) REVERT: E 256 LEU cc_start: 0.8950 (mm) cc_final: 0.8683 (mm) REVERT: E 287 TYR cc_start: 0.8844 (t80) cc_final: 0.8517 (t80) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.0831 time to fit residues: 56.7912 Evaluate side-chains 362 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083307 restraints weight = 36370.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085868 restraints weight = 24299.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087613 restraints weight = 18131.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089015 restraints weight = 14745.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090016 restraints weight = 12519.065| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12857 Z= 0.128 Angle : 0.696 11.216 17655 Z= 0.339 Chirality : 0.047 0.215 2167 Planarity : 0.003 0.029 2122 Dihedral : 5.203 54.466 1855 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1610 helix: 1.32 (0.22), residues: 525 sheet: -0.76 (0.27), residues: 410 loop : -1.22 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 249 TYR 0.030 0.001 TYR D 252 PHE 0.027 0.002 PHE A 289 TRP 0.029 0.001 TRP D 65 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00286 (12848) covalent geometry : angle 0.69284 (17633) SS BOND : bond 0.00203 ( 5) SS BOND : angle 2.05013 ( 10) hydrogen bonds : bond 0.03745 ( 589) hydrogen bonds : angle 4.55991 ( 1665) link_NAG-ASN : bond 0.00645 ( 4) link_NAG-ASN : angle 2.19254 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 428 time to evaluate : 0.496 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 21 ILE cc_start: 0.9486 (tp) cc_final: 0.9266 (mm) REVERT: A 125 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8385 (tttt) REVERT: A 173 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7905 (tp-100) REVERT: A 234 PHE cc_start: 0.8913 (t80) cc_final: 0.8664 (t80) REVERT: A 241 PHE cc_start: 0.8573 (m-80) cc_final: 0.8179 (m-10) REVERT: A 287 TYR cc_start: 0.8427 (t80) cc_final: 0.7968 (t80) REVERT: A 296 LEU cc_start: 0.9078 (mt) cc_final: 0.8800 (mt) REVERT: A 425 PHE cc_start: 0.8580 (t80) cc_final: 0.8342 (t80) REVERT: B 72 ASP cc_start: 0.8665 (t70) cc_final: 0.8400 (t0) REVERT: B 225 PHE cc_start: 0.8519 (m-80) cc_final: 0.8317 (m-80) REVERT: B 227 MET cc_start: 0.8441 (ttm) cc_final: 0.7332 (tpp) REVERT: B 256 LEU cc_start: 0.9015 (mm) cc_final: 0.8754 (mm) REVERT: B 266 MET cc_start: 0.8990 (ppp) cc_final: 0.8515 (ppp) REVERT: B 287 TYR cc_start: 0.8467 (t80) cc_final: 0.8101 (t80) REVERT: C 151 MET cc_start: 0.8507 (ttp) cc_final: 0.8277 (ttm) REVERT: C 187 VAL cc_start: 0.9608 (t) cc_final: 0.9110 (t) REVERT: C 256 LEU cc_start: 0.8958 (mm) cc_final: 0.8694 (mm) REVERT: C 287 TYR cc_start: 0.8627 (t80) cc_final: 0.8167 (t80) REVERT: C 429 LEU cc_start: 0.8942 (mt) cc_final: 0.8637 (mt) REVERT: C 435 ILE cc_start: 0.8703 (pt) cc_final: 0.8424 (tp) REVERT: D 65 TRP cc_start: 0.9319 (p90) cc_final: 0.9081 (p90) REVERT: D 103 PHE cc_start: 0.8620 (m-80) cc_final: 0.7981 (m-80) REVERT: D 155 VAL cc_start: 0.9081 (p) cc_final: 0.8838 (p) REVERT: D 266 MET cc_start: 0.9275 (ptp) cc_final: 0.8947 (ptt) REVERT: D 287 TYR cc_start: 0.8756 (t80) cc_final: 0.8337 (t80) REVERT: D 425 PHE cc_start: 0.8540 (t80) cc_final: 0.8219 (t80) REVERT: D 429 LEU cc_start: 0.8988 (mt) cc_final: 0.8776 (mt) REVERT: E 125 LYS cc_start: 0.6644 (tptt) cc_final: 0.6317 (tptp) REVERT: E 151 MET cc_start: 0.8364 (ttp) cc_final: 0.8061 (ttp) REVERT: E 196 GLN cc_start: 0.9143 (tp40) cc_final: 0.8768 (tp40) REVERT: E 215 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8107 (mmmm) REVERT: E 225 PHE cc_start: 0.8516 (m-80) cc_final: 0.8125 (m-80) REVERT: E 235 LEU cc_start: 0.9439 (mt) cc_final: 0.9171 (mt) REVERT: E 238 LEU cc_start: 0.8947 (mp) cc_final: 0.8719 (mp) REVERT: E 287 TYR cc_start: 0.8894 (t80) cc_final: 0.8545 (t80) REVERT: E 291 MET cc_start: 0.9150 (mmt) cc_final: 0.8643 (mmm) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.0856 time to fit residues: 58.1511 Evaluate side-chains 375 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 277 ASN B 304 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081916 restraints weight = 36666.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084434 restraints weight = 24545.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086227 restraints weight = 18318.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087566 restraints weight = 14809.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088535 restraints weight = 12586.959| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12857 Z= 0.165 Angle : 0.701 10.131 17655 Z= 0.351 Chirality : 0.046 0.201 2167 Planarity : 0.004 0.028 2122 Dihedral : 5.258 52.988 1855 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.08 % Allowed : 1.67 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1610 helix: 1.36 (0.23), residues: 525 sheet: -0.76 (0.27), residues: 410 loop : -1.21 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.036 0.002 TYR D 252 PHE 0.035 0.002 PHE D 289 TRP 0.032 0.002 TRP C 65 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00369 (12848) covalent geometry : angle 0.69694 (17633) SS BOND : bond 0.00184 ( 5) SS BOND : angle 2.08257 ( 10) hydrogen bonds : bond 0.03946 ( 589) hydrogen bonds : angle 4.61548 ( 1665) link_NAG-ASN : bond 0.00435 ( 4) link_NAG-ASN : angle 2.23361 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 0.475 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 21 ILE cc_start: 0.9460 (tp) cc_final: 0.9243 (mm) REVERT: A 72 ASP cc_start: 0.8466 (t0) cc_final: 0.7426 (t0) REVERT: A 103 PHE cc_start: 0.8749 (m-80) cc_final: 0.8530 (m-80) REVERT: A 125 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8627 (tttm) REVERT: A 127 MET cc_start: 0.7518 (ttt) cc_final: 0.7221 (ttt) REVERT: A 173 GLN cc_start: 0.8324 (tp-100) cc_final: 0.8050 (tp-100) REVERT: A 215 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8048 (mmmt) REVERT: A 241 PHE cc_start: 0.8684 (m-80) cc_final: 0.8481 (m-10) REVERT: A 287 TYR cc_start: 0.8601 (t80) cc_final: 0.7988 (t80) REVERT: A 296 LEU cc_start: 0.9161 (mt) cc_final: 0.8822 (mt) REVERT: A 425 PHE cc_start: 0.8654 (t80) cc_final: 0.8367 (t80) REVERT: B 72 ASP cc_start: 0.8715 (t70) cc_final: 0.8440 (t0) REVERT: B 227 MET cc_start: 0.8487 (ttm) cc_final: 0.8282 (ttm) REVERT: B 287 TYR cc_start: 0.8624 (t80) cc_final: 0.8289 (t80) REVERT: C 65 TRP cc_start: 0.9401 (p90) cc_final: 0.8990 (p90) REVERT: C 69 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7168 (mm-30) REVERT: C 151 MET cc_start: 0.8404 (ttp) cc_final: 0.8169 (ttm) REVERT: C 231 LEU cc_start: 0.9089 (mt) cc_final: 0.8839 (mt) REVERT: C 256 LEU cc_start: 0.8978 (mm) cc_final: 0.8752 (mm) REVERT: C 287 TYR cc_start: 0.8729 (t80) cc_final: 0.8288 (t80) REVERT: C 429 LEU cc_start: 0.8981 (mt) cc_final: 0.8675 (mt) REVERT: C 435 ILE cc_start: 0.8806 (pt) cc_final: 0.8480 (tp) REVERT: D 65 TRP cc_start: 0.9278 (p90) cc_final: 0.9073 (p90) REVERT: D 103 PHE cc_start: 0.8720 (m-80) cc_final: 0.8187 (m-80) REVERT: D 155 VAL cc_start: 0.9140 (p) cc_final: 0.8867 (p) REVERT: D 227 MET cc_start: 0.8534 (ttm) cc_final: 0.8095 (tpp) REVERT: D 266 MET cc_start: 0.9244 (ptp) cc_final: 0.8887 (ptt) REVERT: D 287 TYR cc_start: 0.8917 (t80) cc_final: 0.8418 (t80) REVERT: D 425 PHE cc_start: 0.8641 (t80) cc_final: 0.8435 (t80) REVERT: D 429 LEU cc_start: 0.9111 (mt) cc_final: 0.8831 (mt) REVERT: E 125 LYS cc_start: 0.6787 (tptt) cc_final: 0.6326 (tptp) REVERT: E 151 MET cc_start: 0.8371 (ttp) cc_final: 0.8096 (ttp) REVERT: E 196 GLN cc_start: 0.9139 (tp40) cc_final: 0.8745 (tp40) REVERT: E 215 LYS cc_start: 0.8456 (mmmm) cc_final: 0.7924 (mmmm) REVERT: E 225 PHE cc_start: 0.8559 (m-80) cc_final: 0.8076 (m-80) REVERT: E 235 LEU cc_start: 0.9504 (mt) cc_final: 0.9083 (mm) REVERT: E 238 LEU cc_start: 0.8857 (mp) cc_final: 0.8596 (mp) REVERT: E 287 TYR cc_start: 0.8927 (t80) cc_final: 0.8517 (t80) REVERT: E 291 MET cc_start: 0.9230 (mmt) cc_final: 0.8755 (mmm) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.0771 time to fit residues: 51.6049 Evaluate side-chains 356 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 10.0000 chunk 79 optimal weight: 0.0370 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081517 restraints weight = 36960.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084045 restraints weight = 24645.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085893 restraints weight = 18409.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087191 restraints weight = 14819.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088207 restraints weight = 12674.662| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12857 Z= 0.156 Angle : 0.719 12.329 17655 Z= 0.354 Chirality : 0.047 0.202 2167 Planarity : 0.003 0.028 2122 Dihedral : 5.349 54.372 1855 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 0.08 % Allowed : 0.71 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.21), residues: 1610 helix: 1.27 (0.22), residues: 525 sheet: -0.79 (0.26), residues: 440 loop : -1.24 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 216 TYR 0.026 0.002 TYR E 67 PHE 0.031 0.002 PHE E 234 TRP 0.021 0.002 TRP C 65 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00355 (12848) covalent geometry : angle 0.71589 (17633) SS BOND : bond 0.00170 ( 5) SS BOND : angle 2.11045 ( 10) hydrogen bonds : bond 0.03990 ( 589) hydrogen bonds : angle 4.64257 ( 1665) link_NAG-ASN : bond 0.00485 ( 4) link_NAG-ASN : angle 2.15993 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 0.551 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: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9488 (tp) cc_final: 0.9260 (mm) REVERT: A 103 PHE cc_start: 0.8739 (m-80) cc_final: 0.8521 (m-80) REVERT: A 125 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8542 (tttt) REVERT: A 287 TYR cc_start: 0.8526 (t80) cc_final: 0.8017 (t80) REVERT: A 425 PHE cc_start: 0.8627 (t80) cc_final: 0.8258 (t80) REVERT: B 69 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 72 ASP cc_start: 0.8709 (t70) cc_final: 0.8455 (t0) REVERT: B 117 LEU cc_start: 0.9218 (tp) cc_final: 0.9013 (tt) REVERT: B 266 MET cc_start: 0.8976 (ppp) cc_final: 0.8652 (ppp) REVERT: B 268 SER cc_start: 0.9192 (p) cc_final: 0.8982 (p) REVERT: B 287 TYR cc_start: 0.8566 (t80) cc_final: 0.8260 (t80) REVERT: C 65 TRP cc_start: 0.9441 (p90) cc_final: 0.9025 (p90) REVERT: C 231 LEU cc_start: 0.9099 (mt) cc_final: 0.8842 (mt) REVERT: C 256 LEU cc_start: 0.8955 (mm) cc_final: 0.8689 (mm) REVERT: C 287 TYR cc_start: 0.8695 (t80) cc_final: 0.8304 (t80) REVERT: C 429 LEU cc_start: 0.8993 (mt) cc_final: 0.8703 (mt) REVERT: C 435 ILE cc_start: 0.8830 (pt) cc_final: 0.8531 (tt) REVERT: D 103 PHE cc_start: 0.8732 (m-80) cc_final: 0.8221 (m-80) REVERT: D 227 MET cc_start: 0.8529 (ttm) cc_final: 0.8122 (tpp) REVERT: D 266 MET cc_start: 0.9283 (ptp) cc_final: 0.8558 (ptm) REVERT: D 269 ASP cc_start: 0.8142 (m-30) cc_final: 0.7839 (p0) REVERT: D 287 TYR cc_start: 0.8786 (t80) cc_final: 0.8361 (t80) REVERT: D 429 LEU cc_start: 0.9131 (mt) cc_final: 0.8848 (mt) REVERT: E 125 LYS cc_start: 0.6834 (tptt) cc_final: 0.6398 (tptp) REVERT: E 151 MET cc_start: 0.8448 (ttp) cc_final: 0.8159 (ttp) REVERT: E 196 GLN cc_start: 0.9094 (tp40) cc_final: 0.8735 (tp40) REVERT: E 215 LYS cc_start: 0.8394 (mmmm) cc_final: 0.7814 (mmmm) REVERT: E 225 PHE cc_start: 0.8529 (m-80) cc_final: 0.8011 (m-80) REVERT: E 235 LEU cc_start: 0.9570 (mt) cc_final: 0.8998 (mm) REVERT: E 238 LEU cc_start: 0.8810 (mp) cc_final: 0.8587 (mp) REVERT: E 252 TYR cc_start: 0.8775 (t80) cc_final: 0.8426 (t80) REVERT: E 287 TYR cc_start: 0.8840 (t80) cc_final: 0.8483 (t80) REVERT: E 291 MET cc_start: 0.9180 (mmt) cc_final: 0.8694 (mmm) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.0843 time to fit residues: 56.6639 Evaluate side-chains 362 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 40 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 134 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 0.0000 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 40 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082259 restraints weight = 36921.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084821 restraints weight = 24800.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.086670 restraints weight = 18565.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.088026 restraints weight = 15020.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088920 restraints weight = 12777.425| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12857 Z= 0.137 Angle : 0.720 11.692 17655 Z= 0.354 Chirality : 0.046 0.210 2167 Planarity : 0.003 0.030 2122 Dihedral : 5.482 54.995 1855 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 0.08 % Allowed : 0.56 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1610 helix: 1.21 (0.22), residues: 525 sheet: -0.76 (0.26), residues: 440 loop : -1.24 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 216 TYR 0.026 0.001 TYR E 67 PHE 0.038 0.002 PHE D 289 TRP 0.029 0.002 TRP E 128 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00314 (12848) covalent geometry : angle 0.71630 (17633) SS BOND : bond 0.00177 ( 5) SS BOND : angle 2.20414 ( 10) hydrogen bonds : bond 0.03911 ( 589) hydrogen bonds : angle 4.60556 ( 1665) link_NAG-ASN : bond 0.00562 ( 4) link_NAG-ASN : angle 2.07858 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 0.480 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8528 (tttt) REVERT: A 215 LYS cc_start: 0.8294 (mmmt) cc_final: 0.8073 (mmmt) REVERT: A 287 TYR cc_start: 0.8445 (t80) cc_final: 0.8002 (t80) REVERT: B 69 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 72 ASP cc_start: 0.8687 (t70) cc_final: 0.8469 (t0) REVERT: B 266 MET cc_start: 0.8983 (ppp) cc_final: 0.8734 (ppp) REVERT: B 287 TYR cc_start: 0.8525 (t80) cc_final: 0.8230 (t80) REVERT: B 291 MET cc_start: 0.8975 (mmm) cc_final: 0.8722 (mmm) REVERT: C 65 TRP cc_start: 0.9423 (p90) cc_final: 0.9029 (p90) REVERT: C 231 LEU cc_start: 0.9084 (mt) cc_final: 0.8854 (mt) REVERT: C 287 TYR cc_start: 0.8713 (t80) cc_final: 0.8289 (t80) REVERT: C 429 LEU cc_start: 0.8981 (mt) cc_final: 0.8690 (mt) REVERT: C 435 ILE cc_start: 0.8833 (pt) cc_final: 0.8570 (tt) REVERT: D 103 PHE cc_start: 0.8632 (m-80) cc_final: 0.8056 (m-80) REVERT: D 227 MET cc_start: 0.8504 (ttm) cc_final: 0.8145 (tpp) REVERT: D 266 MET cc_start: 0.9162 (ptp) cc_final: 0.8169 (ptm) REVERT: D 287 TYR cc_start: 0.8818 (t80) cc_final: 0.8389 (t80) REVERT: D 425 PHE cc_start: 0.8474 (t80) cc_final: 0.8208 (t80) REVERT: D 429 LEU cc_start: 0.9103 (mt) cc_final: 0.8889 (mt) REVERT: E 125 LYS cc_start: 0.6790 (tptt) cc_final: 0.6350 (tptp) REVERT: E 129 VAL cc_start: 0.9409 (t) cc_final: 0.9207 (t) REVERT: E 151 MET cc_start: 0.8459 (ttp) cc_final: 0.8211 (ttp) REVERT: E 196 GLN cc_start: 0.9105 (tp40) cc_final: 0.8727 (tp40) REVERT: E 215 LYS cc_start: 0.8425 (mmmm) cc_final: 0.7882 (mmmm) REVERT: E 225 PHE cc_start: 0.8530 (m-80) cc_final: 0.7948 (m-80) REVERT: E 235 LEU cc_start: 0.9571 (mt) cc_final: 0.9166 (mm) REVERT: E 238 LEU cc_start: 0.8809 (mp) cc_final: 0.8603 (mp) REVERT: E 287 TYR cc_start: 0.8832 (t80) cc_final: 0.8345 (t80) REVERT: E 291 MET cc_start: 0.9172 (mmt) cc_final: 0.8660 (mmm) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.0794 time to fit residues: 52.4797 Evaluate side-chains 367 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 0.0010 chunk 76 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 40 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS E 58 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.103205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081580 restraints weight = 37235.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084130 restraints weight = 24836.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.085984 restraints weight = 18568.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087221 restraints weight = 14966.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088254 restraints weight = 12843.377| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12857 Z= 0.159 Angle : 0.719 10.320 17655 Z= 0.357 Chirality : 0.047 0.202 2167 Planarity : 0.004 0.031 2122 Dihedral : 5.565 59.057 1855 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 0.24 % Allowed : 0.63 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.21), residues: 1610 helix: 1.10 (0.22), residues: 525 sheet: -0.80 (0.26), residues: 440 loop : -1.23 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.023 0.001 TYR E 287 PHE 0.027 0.002 PHE E 234 TRP 0.044 0.002 TRP E 128 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00365 (12848) covalent geometry : angle 0.71540 (17633) SS BOND : bond 0.00260 ( 5) SS BOND : angle 2.30993 ( 10) hydrogen bonds : bond 0.04039 ( 589) hydrogen bonds : angle 4.69065 ( 1665) link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 2.01284 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.32 seconds wall clock time: 39 minutes 51.37 seconds (2391.37 seconds total)