Starting phenix.real_space_refine on Fri Jul 3 06:39:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_16308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_16308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_16308.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_16308.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_16308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_16308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bx5_16308/07_2026/8bx5_16308.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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: 3.11, per 1000 atoms: 0.25 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: 0.69 Conformation dependent library (CDL) restraints added in 542.9 milliseconds 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: 0.30 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: 1.85 Time building geometry restraints manager: 0.94 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 - 16.04: 6738 16.04 - 32.08: 524 32.08 - 48.12: 121 48.12 - 64.16: 29 64.16 - 80.20: 5 Dihedral angle restraints: 7417 sinusoidal: 2572 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 7414 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: 0.310 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.070 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 : 12.697 80.198 4272 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 are 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/Z covalent geometry : bond 0.00347 / 0.18 (12848) covalent geometry : angle 0.78430 / 0.41 (17633) SS BOND : bond 0.00247 / 0.11 ( 5) SS BOND : angle 1.89906 / 1.21 ( 10) hydrogen bonds : bond 0.11792 / 8.68 ( 589) hydrogen bonds : angle 5.37505 / 3.81 ( 1665) link_NAG-ASN : bond 0.01897 / 0.95 ( 4) link_NAG-ASN : angle 6.84784 / 4.61 ( 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 : 0.403 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: 0.8742 (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: 0.8049 (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: 0.0741 time to fit residues: 53.8710 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 : 0.392 ------------------------------------------------------------------------------- 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... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083430 restraints weight = 37297.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086025 restraints weight = 24660.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087882 restraints weight = 18266.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.089217 restraints weight = 14674.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090177 restraints weight = 12454.887| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12857 Z= 0.167 Angle : 0.683 12.789 17655 Z= 0.336 Chirality : 0.048 0.416 2167 Planarity : 0.004 0.038 2122 Dihedral : 4.185 18.074 1771 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 0.08 % Allowed : 6.67 % Favored : 93.25 % 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 are not related in a simple way. whole: -0.66 (0.21), residues: 1610 helix: 1.30 (0.22), residues: 525 sheet: -1.10 (0.26), residues: 420 loop : -1.35 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 133 TYR 0.020 0.001 TYR D 252 PHE 0.031 0.002 PHE C 428 TRP 0.017 0.001 TRP C 159 HIS 0.008 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (12848) covalent geometry : angle 0.67693 / 0.33 (17633) SS BOND : bond 0.00138 / 0.07 ( 5) SS BOND : angle 1.96243 / 1.23 ( 10) hydrogen bonds : bond 0.04046 / 2.80 ( 589) hydrogen bonds : angle 4.83645 / 3.45 ( 1665) link_NAG-ASN : bond 0.00730 / 0.36 ( 4) link_NAG-ASN : angle 3.04126 / 1.74 ( 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 411 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8098 (tttm) REVERT: A 128 TRP cc_start: 0.7768 (t60) cc_final: 0.6762 (t60) REVERT: A 161 HIS cc_start: 0.7359 (p90) cc_final: 0.7027 (p-80) REVERT: A 173 GLN cc_start: 0.8305 (tp-100) cc_final: 0.8031 (tp-100) REVERT: A 215 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7998 (mmmt) REVERT: A 234 PHE cc_start: 0.8723 (t80) cc_final: 0.8464 (t80) REVERT: A 271 MET cc_start: 0.8781 (tmm) cc_final: 0.8553 (tmm) REVERT: A 287 TYR cc_start: 0.8503 (t80) cc_final: 0.8213 (t80) REVERT: A 296 LEU cc_start: 0.9110 (mt) cc_final: 0.8898 (mt) REVERT: A 425 PHE cc_start: 0.8497 (t80) cc_final: 0.8274 (t80) REVERT: B 85 LEU cc_start: 0.9010 (tp) cc_final: 0.8789 (pp) REVERT: B 125 LYS cc_start: 0.8417 (tttp) cc_final: 0.8173 (tttm) REVERT: B 213 LYS cc_start: 0.8844 (mmpt) cc_final: 0.8634 (mmmt) REVERT: B 266 MET cc_start: 0.9017 (ppp) cc_final: 0.8772 (ppp) REVERT: B 269 ASP cc_start: 0.7583 (m-30) cc_final: 0.7313 (m-30) REVERT: C 151 MET cc_start: 0.8362 (ttp) cc_final: 0.8111 (ttm) REVERT: C 231 LEU cc_start: 0.9003 (mt) cc_final: 0.8775 (mt) REVERT: C 266 MET cc_start: 0.9231 (ptp) cc_final: 0.8997 (ptm) REVERT: C 287 TYR cc_start: 0.8493 (t80) cc_final: 0.8066 (t80) REVERT: C 429 LEU cc_start: 0.8801 (mt) cc_final: 0.8544 (mt) REVERT: C 435 ILE cc_start: 0.8703 (pt) cc_final: 0.8343 (tp) REVERT: D 103 PHE cc_start: 0.8429 (m-80) cc_final: 0.7875 (m-80) REVERT: D 265 MET cc_start: 0.8494 (ttp) cc_final: 0.8240 (ttp) REVERT: D 266 MET cc_start: 0.9313 (ptp) cc_final: 0.9044 (ptt) REVERT: D 271 MET cc_start: 0.8959 (tmm) cc_final: 0.8732 (tmm) REVERT: D 287 TYR cc_start: 0.8778 (t80) cc_final: 0.8452 (t80) REVERT: D 301 MET cc_start: 0.8106 (mmm) cc_final: 0.7685 (mmm) REVERT: D 425 PHE cc_start: 0.8308 (t80) cc_final: 0.8060 (t80) REVERT: D 429 LEU cc_start: 0.9081 (mt) cc_final: 0.8879 (mt) REVERT: E 62 THR cc_start: 0.9231 (p) cc_final: 0.9030 (p) REVERT: E 151 MET cc_start: 0.8670 (ttp) cc_final: 0.8395 (ttp) REVERT: E 215 LYS cc_start: 0.8304 (mmmm) cc_final: 0.7868 (mmmm) REVERT: E 225 PHE cc_start: 0.8667 (m-80) cc_final: 0.8309 (m-80) REVERT: E 227 MET cc_start: 0.8256 (ttm) cc_final: 0.7980 (ttm) REVERT: E 235 LEU cc_start: 0.9517 (mt) cc_final: 0.9166 (mt) REVERT: E 287 TYR cc_start: 0.8609 (t80) cc_final: 0.8407 (t80) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.0721 time to fit residues: 46.6974 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 : 0.418 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 chunk 63 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.083773 restraints weight = 36962.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.086383 restraints weight = 24379.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.087970 restraints weight = 18032.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.089469 restraints weight = 14858.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.090482 restraints weight = 12499.469| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12857 Z= 0.139 Angle : 0.678 10.950 17655 Z= 0.331 Chirality : 0.046 0.341 2167 Planarity : 0.003 0.030 2122 Dihedral : 4.119 18.852 1771 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % 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 are not related in a simple way. whole: -0.63 (0.21), residues: 1610 helix: 1.26 (0.22), residues: 525 sheet: -1.01 (0.26), residues: 420 loop : -1.32 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 249 TYR 0.014 0.001 TYR D 252 PHE 0.032 0.002 PHE D 289 TRP 0.018 0.001 TRP B 185 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12848) covalent geometry : angle 0.67251 / 0.33 (17633) SS BOND : bond 0.00118 / 0.08 ( 5) SS BOND : angle 2.26679 / 1.36 ( 10) hydrogen bonds : bond 0.03931 / 2.72 ( 589) hydrogen bonds : angle 4.75420 / 3.39 ( 1665) link_NAG-ASN : bond 0.00612 / 0.31 ( 4) link_NAG-ASN : angle 2.56963 / 1.47 ( 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 : 0.343 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 173 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7941 (tp-100) REVERT: A 215 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7960 (mmmt) REVERT: A 234 PHE cc_start: 0.8773 (t80) cc_final: 0.8544 (t80) REVERT: A 241 PHE cc_start: 0.8551 (m-80) cc_final: 0.8341 (m-10) REVERT: A 265 MET cc_start: 0.8487 (ttt) cc_final: 0.8064 (ttm) REVERT: A 287 TYR cc_start: 0.8473 (t80) cc_final: 0.8173 (t80) REVERT: A 296 LEU cc_start: 0.9039 (mt) cc_final: 0.8723 (mt) REVERT: B 72 ASP cc_start: 0.8666 (t70) cc_final: 0.8297 (t0) REVERT: B 85 LEU cc_start: 0.9097 (tp) cc_final: 0.8731 (pp) REVERT: B 103 PHE cc_start: 0.9094 (m-80) cc_final: 0.8785 (m-80) REVERT: B 266 MET cc_start: 0.9031 (ppp) cc_final: 0.8575 (ppp) REVERT: B 268 SER cc_start: 0.9245 (p) cc_final: 0.8966 (t) REVERT: B 269 ASP cc_start: 0.7640 (m-30) cc_final: 0.7389 (m-30) REVERT: B 287 TYR cc_start: 0.8582 (t80) cc_final: 0.8222 (t80) REVERT: B 429 LEU cc_start: 0.9026 (pp) cc_final: 0.8764 (pp) REVERT: C 151 MET cc_start: 0.8457 (ttp) cc_final: 0.8128 (ttm) REVERT: C 266 MET cc_start: 0.9234 (ptp) cc_final: 0.9005 (ptm) REVERT: C 269 ASP cc_start: 0.8309 (m-30) cc_final: 0.8098 (m-30) REVERT: C 287 TYR cc_start: 0.8665 (t80) cc_final: 0.8226 (t80) REVERT: C 429 LEU cc_start: 0.8827 (mt) cc_final: 0.8558 (mt) REVERT: C 435 ILE cc_start: 0.8654 (pt) cc_final: 0.8321 (tp) REVERT: D 102 LEU cc_start: 0.9241 (tt) cc_final: 0.8882 (tt) REVERT: D 103 PHE cc_start: 0.8560 (m-80) cc_final: 0.7936 (m-80) REVERT: D 252 TYR cc_start: 0.8832 (t80) cc_final: 0.8569 (t80) REVERT: D 265 MET cc_start: 0.8316 (ttp) cc_final: 0.8114 (ttp) REVERT: D 266 MET cc_start: 0.9300 (ptp) cc_final: 0.9057 (ptt) REVERT: D 287 TYR cc_start: 0.8802 (t80) cc_final: 0.8406 (t80) REVERT: D 289 PHE cc_start: 0.9077 (t80) cc_final: 0.8773 (t80) REVERT: D 425 PHE cc_start: 0.8342 (t80) cc_final: 0.8077 (t80) REVERT: D 429 LEU cc_start: 0.9088 (mt) cc_final: 0.8879 (mt) REVERT: E 62 THR cc_start: 0.9261 (p) cc_final: 0.8814 (t) REVERT: E 151 MET cc_start: 0.8409 (ttp) cc_final: 0.8077 (ttp) REVERT: E 196 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8770 (tp40) REVERT: E 215 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8256 (mmmm) REVERT: E 225 PHE cc_start: 0.8629 (m-80) cc_final: 0.8201 (m-80) REVERT: E 235 LEU cc_start: 0.9449 (mt) cc_final: 0.9101 (mm) REVERT: E 252 TYR cc_start: 0.8881 (t80) cc_final: 0.8440 (t80) REVERT: E 291 MET cc_start: 0.9136 (mmt) cc_final: 0.8782 (mmt) outliers start: 1 outliers final: 0 residues processed: 429 average time/residue: 0.0713 time to fit residues: 48.6590 Evaluate side-chains 376 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN B 277 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.103711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082553 restraints weight = 37358.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084967 restraints weight = 24639.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.086793 restraints weight = 18429.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088015 restraints weight = 14853.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088990 restraints weight = 12724.494| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12857 Z= 0.166 Angle : 0.662 9.548 17655 Z= 0.330 Chirality : 0.046 0.338 2167 Planarity : 0.003 0.030 2122 Dihedral : 4.172 19.100 1771 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % 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 are not related in a simple way. whole: -0.49 (0.21), residues: 1610 helix: 1.29 (0.22), residues: 525 sheet: -0.82 (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 216 TYR 0.017 0.002 TYR B 284 PHE 0.026 0.002 PHE D 289 TRP 0.026 0.002 TRP C 65 HIS 0.007 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (12848) covalent geometry : angle 0.65711 / 0.33 (17633) SS BOND : bond 0.00560 / 0.29 ( 5) SS BOND : angle 1.97269 / 1.24 ( 10) hydrogen bonds : bond 0.03875 / 2.69 ( 589) hydrogen bonds : angle 4.73257 / 3.38 ( 1665) link_NAG-ASN : bond 0.00555 / 0.28 ( 4) link_NAG-ASN : angle 2.58215 / 1.46 ( 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 424 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 422 time to evaluate : 0.306 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: 0.9550 (tp) cc_final: 0.9338 (mm) REVERT: A 125 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8298 (ttpp) REVERT: A 173 GLN cc_start: 0.8320 (tp-100) cc_final: 0.8043 (tp-100) REVERT: A 234 PHE cc_start: 0.8932 (t80) cc_final: 0.8673 (t80) REVERT: A 266 MET cc_start: 0.9317 (ptp) cc_final: 0.9109 (ptp) REVERT: A 287 TYR cc_start: 0.8540 (t80) cc_final: 0.8183 (t80) REVERT: A 296 LEU cc_start: 0.9060 (mt) cc_final: 0.8747 (mt) REVERT: A 425 PHE cc_start: 0.8663 (t80) cc_final: 0.8342 (t80) REVERT: B 72 ASP cc_start: 0.8814 (t70) cc_final: 0.8189 (t0) REVERT: B 103 PHE cc_start: 0.9145 (m-80) cc_final: 0.8910 (m-80) REVERT: B 266 MET cc_start: 0.9000 (ppp) cc_final: 0.8597 (ppp) REVERT: B 268 SER cc_start: 0.9293 (p) cc_final: 0.9074 (t) REVERT: B 269 ASP cc_start: 0.7599 (m-30) cc_final: 0.7359 (m-30) REVERT: B 287 TYR cc_start: 0.8562 (t80) cc_final: 0.8038 (t80) REVERT: B 429 LEU cc_start: 0.9111 (pp) cc_final: 0.8859 (pp) REVERT: C 65 TRP cc_start: 0.9237 (p90) cc_final: 0.8818 (p90) REVERT: C 151 MET cc_start: 0.8432 (ttp) cc_final: 0.8200 (ttp) REVERT: C 187 VAL cc_start: 0.9560 (t) cc_final: 0.9195 (t) REVERT: C 231 LEU cc_start: 0.9063 (mt) cc_final: 0.8797 (mt) REVERT: C 287 TYR cc_start: 0.8608 (t80) cc_final: 0.8184 (t80) REVERT: C 429 LEU cc_start: 0.8854 (mt) cc_final: 0.8603 (mt) REVERT: C 435 ILE cc_start: 0.8707 (pt) cc_final: 0.8351 (tp) REVERT: D 103 PHE cc_start: 0.8450 (m-80) cc_final: 0.7894 (m-80) REVERT: D 265 MET cc_start: 0.8346 (ttp) cc_final: 0.8131 (ttp) REVERT: D 287 TYR cc_start: 0.8793 (t80) cc_final: 0.8412 (t80) REVERT: D 289 PHE cc_start: 0.9163 (t80) cc_final: 0.8648 (t80) REVERT: D 425 PHE cc_start: 0.8445 (t80) cc_final: 0.8143 (t80) REVERT: D 429 LEU cc_start: 0.9134 (mt) cc_final: 0.8923 (mt) REVERT: E 74 GLN cc_start: 0.8384 (mp10) cc_final: 0.8179 (mp10) REVERT: E 151 MET cc_start: 0.8392 (ttp) cc_final: 0.8084 (ttp) REVERT: E 196 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8727 (tp40) REVERT: E 215 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8156 (mmmm) REVERT: E 225 PHE cc_start: 0.8637 (m-80) cc_final: 0.8228 (m-80) REVERT: E 287 TYR cc_start: 0.8626 (t80) cc_final: 0.8417 (t80) REVERT: E 291 MET cc_start: 0.9145 (mmt) cc_final: 0.8726 (mmt) REVERT: E 296 LEU cc_start: 0.9314 (mt) cc_final: 0.9096 (mt) outliers start: 2 outliers final: 0 residues processed: 423 average time/residue: 0.0646 time to fit residues: 43.9848 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 : 0.310 ------------------------------------------------------------------------------- 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: 0.7980 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.100551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079315 restraints weight = 38078.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081786 restraints weight = 25191.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083573 restraints weight = 18770.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084775 restraints weight = 15171.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085657 restraints weight = 13067.014| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12857 Z= 0.220 Angle : 0.713 10.270 17655 Z= 0.356 Chirality : 0.047 0.336 2167 Planarity : 0.004 0.030 2122 Dihedral : 4.369 21.492 1771 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.90 % Rotamer: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.56 % 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 are not related in a simple way. whole: -0.53 (0.21), residues: 1610 helix: 1.25 (0.22), residues: 525 sheet: -0.82 (0.27), residues: 400 loop : -1.29 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 216 TYR 0.018 0.002 TYR D 252 PHE 0.023 0.002 PHE D 289 TRP 0.036 0.002 TRP D 65 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (12848) covalent geometry : angle 0.70798 / 0.36 (17633) SS BOND : bond 0.00230 / 0.11 ( 5) SS BOND : angle 2.21004 / 1.41 ( 10) hydrogen bonds : bond 0.04137 / 2.84 ( 589) hydrogen bonds : angle 4.92500 / 3.48 ( 1665) link_NAG-ASN : bond 0.00412 / 0.20 ( 4) link_NAG-ASN : angle 2.60026 / 1.49 ( 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 409 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 0.440 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: 0.9522 (tp) cc_final: 0.9268 (mm) REVERT: A 125 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8423 (tttt) REVERT: A 173 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8060 (tp-100) REVERT: A 265 MET cc_start: 0.8577 (ttt) cc_final: 0.8300 (ttm) REVERT: A 287 TYR cc_start: 0.8420 (t80) cc_final: 0.7982 (t80) REVERT: A 296 LEU cc_start: 0.9159 (mt) cc_final: 0.8779 (mt) REVERT: A 425 PHE cc_start: 0.8722 (t80) cc_final: 0.8391 (t80) REVERT: B 72 ASP cc_start: 0.8801 (t70) cc_final: 0.8019 (t0) REVERT: B 117 LEU cc_start: 0.9227 (tp) cc_final: 0.9022 (tt) REVERT: B 266 MET cc_start: 0.9025 (ppp) cc_final: 0.8618 (ppp) REVERT: B 268 SER cc_start: 0.9325 (p) cc_final: 0.9014 (t) REVERT: B 287 TYR cc_start: 0.8603 (t80) cc_final: 0.7971 (t80) REVERT: C 65 TRP cc_start: 0.9393 (p90) cc_final: 0.9114 (p90) REVERT: C 151 MET cc_start: 0.8595 (ttp) cc_final: 0.8388 (ttp) REVERT: C 215 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8362 (mmmt) REVERT: C 256 LEU cc_start: 0.8972 (mm) cc_final: 0.8711 (mm) REVERT: C 265 MET cc_start: 0.8569 (ttp) cc_final: 0.8362 (ttp) REVERT: C 269 ASP cc_start: 0.8413 (m-30) cc_final: 0.8189 (m-30) REVERT: C 287 TYR cc_start: 0.8610 (t80) cc_final: 0.8225 (t80) REVERT: C 429 LEU cc_start: 0.9081 (mt) cc_final: 0.8745 (mt) REVERT: C 435 ILE cc_start: 0.8978 (pt) cc_final: 0.8587 (tp) REVERT: D 103 PHE cc_start: 0.8678 (m-80) cc_final: 0.8090 (m-80) REVERT: D 287 TYR cc_start: 0.8803 (t80) cc_final: 0.8406 (t80) REVERT: D 425 PHE cc_start: 0.8569 (t80) cc_final: 0.8306 (t80) REVERT: D 429 LEU cc_start: 0.9202 (mt) cc_final: 0.8936 (mt) REVERT: E 74 GLN cc_start: 0.8499 (mp10) cc_final: 0.8287 (mp10) REVERT: E 127 MET cc_start: 0.6472 (mmt) cc_final: 0.6035 (ttt) REVERT: E 151 MET cc_start: 0.8543 (ttp) cc_final: 0.8236 (ttp) REVERT: E 196 GLN cc_start: 0.9098 (tp40) cc_final: 0.8694 (tp40) REVERT: E 215 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8230 (mmmm) REVERT: E 227 MET cc_start: 0.8439 (ttm) cc_final: 0.8022 (ttm) REVERT: E 252 TYR cc_start: 0.8881 (t80) cc_final: 0.8513 (t80) REVERT: E 287 TYR cc_start: 0.8659 (t80) cc_final: 0.8407 (t80) REVERT: E 291 MET cc_start: 0.9100 (mmt) cc_final: 0.8664 (mmt) REVERT: E 296 LEU cc_start: 0.9342 (mt) cc_final: 0.9044 (mt) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.0692 time to fit residues: 45.3927 Evaluate side-chains 340 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 10.0000 chunk 68 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.0050 chunk 132 optimal weight: 10.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3610 r_free = 0.3610 target = 0.103818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082517 restraints weight = 36749.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085051 restraints weight = 24240.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.086818 restraints weight = 18037.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088167 restraints weight = 14632.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089010 restraints weight = 12425.889| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2628 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= 0.128 Angle : 0.690 13.311 17655 Z= 0.337 Chirality : 0.047 0.281 2167 Planarity : 0.003 0.031 2122 Dihedral : 4.233 19.482 1771 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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 are not related in a simple way. whole: -0.54 (0.21), residues: 1610 helix: 1.30 (0.22), residues: 525 sheet: -0.90 (0.26), residues: 410 loop : -1.29 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 249 TYR 0.033 0.001 TYR D 252 PHE 0.028 0.002 PHE B 428 TRP 0.018 0.001 TRP D 65 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (12848) covalent geometry : angle 0.68556 / 0.34 (17633) SS BOND : bond 0.00187 / 0.11 ( 5) SS BOND : angle 2.27861 / 1.44 ( 10) hydrogen bonds : bond 0.03826 / 2.64 ( 589) hydrogen bonds : angle 4.64402 / 3.29 ( 1665) link_NAG-ASN : bond 0.00776 / 0.39 ( 4) link_NAG-ASN : angle 2.51823 / 1.42 ( 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 425 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9473 (tp) cc_final: 0.9245 (mm) REVERT: A 125 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8419 (tttt) REVERT: A 265 MET cc_start: 0.8467 (ttt) cc_final: 0.8152 (ttm) REVERT: A 287 TYR cc_start: 0.8341 (t80) cc_final: 0.8003 (t80) REVERT: A 296 LEU cc_start: 0.9062 (mt) cc_final: 0.8672 (mt) REVERT: A 425 PHE cc_start: 0.8548 (t80) cc_final: 0.8241 (t80) REVERT: B 266 MET cc_start: 0.8922 (ppp) cc_final: 0.8523 (ppp) REVERT: B 287 TYR cc_start: 0.8393 (t80) cc_final: 0.8170 (t80) REVERT: C 65 TRP cc_start: 0.9395 (p90) cc_final: 0.9089 (p90) REVERT: C 215 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8442 (mmmt) REVERT: C 287 TYR cc_start: 0.8597 (t80) cc_final: 0.8169 (t80) REVERT: C 429 LEU cc_start: 0.9060 (mt) cc_final: 0.8729 (mt) REVERT: C 435 ILE cc_start: 0.8781 (pt) cc_final: 0.8473 (tp) REVERT: D 103 PHE cc_start: 0.8583 (m-80) cc_final: 0.7931 (m-80) REVERT: D 227 MET cc_start: 0.8302 (ttm) cc_final: 0.7652 (tpp) REVERT: D 266 MET cc_start: 0.9214 (ptp) cc_final: 0.8916 (ptt) REVERT: D 287 TYR cc_start: 0.8722 (t80) cc_final: 0.8301 (t80) REVERT: D 425 PHE cc_start: 0.8556 (t80) cc_final: 0.8282 (t80) REVERT: D 429 LEU cc_start: 0.9082 (mt) cc_final: 0.8787 (mt) REVERT: E 151 MET cc_start: 0.8531 (ttp) cc_final: 0.8242 (ttp) REVERT: E 196 GLN cc_start: 0.9092 (tp40) cc_final: 0.8756 (tp40) REVERT: E 215 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8174 (mmmm) REVERT: E 227 MET cc_start: 0.8348 (ttm) cc_final: 0.7997 (ttm) REVERT: E 238 LEU cc_start: 0.8869 (mp) cc_final: 0.8592 (mp) REVERT: E 252 TYR cc_start: 0.8718 (t80) cc_final: 0.8345 (t80) REVERT: E 256 LEU cc_start: 0.8866 (mm) cc_final: 0.8592 (mm) REVERT: E 287 TYR cc_start: 0.8667 (t80) cc_final: 0.8434 (t80) REVERT: E 291 MET cc_start: 0.9133 (mmt) cc_final: 0.8806 (mmt) REVERT: E 296 LEU cc_start: 0.9288 (mt) cc_final: 0.9065 (mt) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.0727 time to fit residues: 49.2969 Evaluate side-chains 354 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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: 9.9990 chunk 86 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 40 optimal weight: 0.0040 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 87 optimal weight: 0.0040 overall best weight: 1.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082550 restraints weight = 37871.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085233 restraints weight = 24912.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087142 restraints weight = 18363.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.088469 restraints weight = 14725.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089309 restraints weight = 12524.653| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2810 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= 0.151 Angle : 0.707 13.808 17655 Z= 0.347 Chirality : 0.047 0.276 2167 Planarity : 0.003 0.030 2122 Dihedral : 4.255 20.539 1771 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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 are not related in a simple way. whole: -0.49 (0.21), residues: 1610 helix: 1.32 (0.22), residues: 525 sheet: -0.83 (0.27), residues: 410 loop : -1.27 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.035 0.002 TYR D 252 PHE 0.023 0.002 PHE A 289 TRP 0.021 0.001 TRP D 159 HIS 0.009 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (12848) covalent geometry : angle 0.70275 / 0.35 (17633) SS BOND : bond 0.00197 / 0.10 ( 5) SS BOND : angle 2.16713 / 1.37 ( 10) hydrogen bonds : bond 0.03883 / 2.68 ( 589) hydrogen bonds : angle 4.66357 / 3.30 ( 1665) link_NAG-ASN : bond 0.00585 / 0.29 ( 4) link_NAG-ASN : angle 2.59815 / 1.45 ( 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 410 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.355 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: 0.9470 (tp) cc_final: 0.9250 (mm) REVERT: A 125 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8444 (tttt) REVERT: A 265 MET cc_start: 0.8559 (ttt) cc_final: 0.8305 (ttm) REVERT: A 287 TYR cc_start: 0.8544 (t80) cc_final: 0.8114 (t80) REVERT: A 296 LEU cc_start: 0.9149 (mt) cc_final: 0.8794 (mt) REVERT: A 425 PHE cc_start: 0.8643 (t80) cc_final: 0.8319 (t80) REVERT: B 225 PHE cc_start: 0.8501 (m-80) cc_final: 0.8041 (m-80) REVERT: B 266 MET cc_start: 0.8995 (ppp) cc_final: 0.8475 (ppp) REVERT: B 287 TYR cc_start: 0.8544 (t80) cc_final: 0.8176 (t80) REVERT: C 65 TRP cc_start: 0.9325 (p90) cc_final: 0.9114 (p90) REVERT: C 151 MET cc_start: 0.8562 (ttp) cc_final: 0.8329 (ttm) REVERT: C 187 VAL cc_start: 0.9583 (t) cc_final: 0.9153 (t) REVERT: C 215 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8446 (mmmt) REVERT: C 239 MET cc_start: 0.8657 (ttt) cc_final: 0.8396 (ttt) REVERT: C 252 TYR cc_start: 0.8842 (t80) cc_final: 0.8617 (t80) REVERT: C 256 LEU cc_start: 0.9022 (mm) cc_final: 0.8736 (mm) REVERT: C 287 TYR cc_start: 0.8619 (t80) cc_final: 0.8217 (t80) REVERT: C 301 MET cc_start: 0.7694 (mmm) cc_final: 0.7405 (mmm) REVERT: C 429 LEU cc_start: 0.9003 (mt) cc_final: 0.8681 (mt) REVERT: C 435 ILE cc_start: 0.8826 (pt) cc_final: 0.8510 (tp) REVERT: D 103 PHE cc_start: 0.8647 (m-80) cc_final: 0.8102 (m-80) REVERT: D 155 VAL cc_start: 0.9262 (p) cc_final: 0.8899 (p) REVERT: D 227 MET cc_start: 0.8143 (ttm) cc_final: 0.7721 (tpp) REVERT: D 266 MET cc_start: 0.9238 (ptp) cc_final: 0.8937 (ptt) REVERT: D 287 TYR cc_start: 0.8779 (t80) cc_final: 0.8360 (t80) REVERT: D 425 PHE cc_start: 0.8627 (t80) cc_final: 0.8358 (t80) REVERT: D 429 LEU cc_start: 0.9170 (mt) cc_final: 0.8874 (mt) REVERT: E 151 MET cc_start: 0.8412 (ttp) cc_final: 0.8098 (ttp) REVERT: E 196 GLN cc_start: 0.9104 (tp40) cc_final: 0.8709 (tp40) REVERT: E 215 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8166 (mmmm) REVERT: E 238 LEU cc_start: 0.8840 (mp) cc_final: 0.8525 (mp) REVERT: E 252 TYR cc_start: 0.8828 (t80) cc_final: 0.8459 (t80) REVERT: E 256 LEU cc_start: 0.8955 (mm) cc_final: 0.8746 (mm) REVERT: E 287 TYR cc_start: 0.8719 (t80) cc_final: 0.8513 (t80) REVERT: E 291 MET cc_start: 0.9141 (mmt) cc_final: 0.8712 (mmt) REVERT: E 296 LEU cc_start: 0.9320 (mt) cc_final: 0.9110 (mt) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.0708 time to fit residues: 46.5527 Evaluate side-chains 349 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 144 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.3637 r_free = 0.3637 target = 0.104915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083489 restraints weight = 37586.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086162 restraints weight = 24682.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088071 restraints weight = 18230.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.089432 restraints weight = 14610.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090268 restraints weight = 12387.430| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2902 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= 0.135 Angle : 0.714 12.459 17655 Z= 0.347 Chirality : 0.047 0.258 2167 Planarity : 0.003 0.030 2122 Dihedral : 4.261 20.589 1771 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.94 % 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 are not related in a simple way. whole: -0.47 (0.21), residues: 1610 helix: 1.28 (0.22), residues: 525 sheet: -0.78 (0.27), 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 0.034 0.001 TYR D 252 PHE 0.044 0.002 PHE D 289 TRP 0.017 0.001 TRP D 159 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12848) covalent geometry : angle 0.71005 / 0.35 (17633) SS BOND : bond 0.00208 / 0.11 ( 5) SS BOND : angle 2.02727 / 1.29 ( 10) hydrogen bonds : bond 0.03879 / 2.64 ( 589) hydrogen bonds : angle 4.59397 / 3.26 ( 1665) link_NAG-ASN : bond 0.00616 / 0.31 ( 4) link_NAG-ASN : angle 2.53449 / 1.42 ( 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 411 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.307 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: 0.9476 (tp) cc_final: 0.9257 (mm) REVERT: A 72 ASP cc_start: 0.8593 (t0) cc_final: 0.7592 (t0) REVERT: A 125 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8448 (tttt) REVERT: A 265 MET cc_start: 0.8624 (ttt) cc_final: 0.8162 (ttm) REVERT: A 287 TYR cc_start: 0.8712 (t80) cc_final: 0.8190 (t80) REVERT: A 296 LEU cc_start: 0.9140 (mt) cc_final: 0.8783 (mt) REVERT: B 69 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 225 PHE cc_start: 0.8639 (m-80) cc_final: 0.8345 (m-80) REVERT: B 266 MET cc_start: 0.9093 (ppp) cc_final: 0.8498 (ppp) REVERT: B 268 SER cc_start: 0.9263 (p) cc_final: 0.8973 (p) REVERT: B 287 TYR cc_start: 0.8572 (t80) cc_final: 0.8203 (t80) REVERT: C 65 TRP cc_start: 0.9325 (p90) cc_final: 0.9082 (p90) REVERT: C 125 LYS cc_start: 0.8210 (tttm) cc_final: 0.7892 (tmtt) REVERT: C 215 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8434 (mmmt) REVERT: C 231 LEU cc_start: 0.9086 (mt) cc_final: 0.8835 (mt) REVERT: C 252 TYR cc_start: 0.8860 (t80) cc_final: 0.8583 (t80) REVERT: C 256 LEU cc_start: 0.8976 (mm) cc_final: 0.8705 (mm) REVERT: C 287 TYR cc_start: 0.8678 (t80) cc_final: 0.8229 (t80) REVERT: C 301 MET cc_start: 0.7877 (mmm) cc_final: 0.7604 (mmm) REVERT: C 429 LEU cc_start: 0.8952 (mt) cc_final: 0.8645 (mt) REVERT: C 435 ILE cc_start: 0.8798 (pt) cc_final: 0.8464 (tp) REVERT: D 103 PHE cc_start: 0.8634 (m-80) cc_final: 0.8078 (m-80) REVERT: D 227 MET cc_start: 0.8230 (ttm) cc_final: 0.7650 (tpp) REVERT: D 266 MET cc_start: 0.9170 (ptp) cc_final: 0.8775 (ptt) REVERT: D 287 TYR cc_start: 0.8863 (t80) cc_final: 0.8337 (t80) REVERT: D 425 PHE cc_start: 0.8669 (t80) cc_final: 0.8332 (t80) REVERT: D 429 LEU cc_start: 0.9075 (mt) cc_final: 0.8760 (mt) REVERT: E 151 MET cc_start: 0.8366 (ttp) cc_final: 0.8071 (ttp) REVERT: E 196 GLN cc_start: 0.9111 (tp40) cc_final: 0.8711 (tp40) REVERT: E 215 LYS cc_start: 0.8411 (mmmm) cc_final: 0.8086 (mmmm) REVERT: E 238 LEU cc_start: 0.8856 (mp) cc_final: 0.8549 (mp) REVERT: E 252 TYR cc_start: 0.8856 (t80) cc_final: 0.8459 (t80) REVERT: E 256 LEU cc_start: 0.8991 (mm) cc_final: 0.8771 (mm) REVERT: E 265 MET cc_start: 0.9160 (ttm) cc_final: 0.8954 (ttt) REVERT: E 287 TYR cc_start: 0.8769 (t80) cc_final: 0.8553 (t80) REVERT: E 291 MET cc_start: 0.9181 (mmt) cc_final: 0.8724 (mmt) REVERT: E 296 LEU cc_start: 0.9329 (mt) cc_final: 0.9112 (mt) outliers start: 1 outliers final: 0 residues processed: 411 average time/residue: 0.0706 time to fit residues: 46.2488 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 : 0.466 ------------------------------------------------------------------------------- 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: 0.8980 chunk 79 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN ** 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 = 0.3616 r_free = 0.3616 target = 0.103535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082132 restraints weight = 37876.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.084805 restraints weight = 24858.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086670 restraints weight = 18347.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087741 restraints weight = 14716.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088947 restraints weight = 12715.889| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3013 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= 0.156 Angle : 0.726 12.206 17655 Z= 0.355 Chirality : 0.047 0.264 2167 Planarity : 0.003 0.030 2122 Dihedral : 4.311 20.670 1771 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % 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 are not related in a simple way. whole: -0.54 (0.21), residues: 1610 helix: 1.23 (0.22), residues: 525 sheet: -0.84 (0.26), residues: 440 loop : -1.27 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.020 0.001 TYR B 223 PHE 0.029 0.002 PHE A 289 TRP 0.016 0.001 TRP D 159 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (12848) covalent geometry : angle 0.72190 / 0.35 (17633) SS BOND : bond 0.00207 / 0.11 ( 5) SS BOND : angle 1.97610 / 1.26 ( 10) hydrogen bonds : bond 0.03929 / 2.69 ( 589) hydrogen bonds : angle 4.65131 / 3.30 ( 1665) link_NAG-ASN : bond 0.00531 / 0.27 ( 4) link_NAG-ASN : angle 2.57561 / 1.44 ( 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 412 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6535 (mm-30) REVERT: A 125 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8601 (tttm) REVERT: A 127 MET cc_start: 0.7468 (ttt) cc_final: 0.6904 (ttt) REVERT: A 265 MET cc_start: 0.8703 (ttt) cc_final: 0.8254 (ttm) REVERT: B 69 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 225 PHE cc_start: 0.8652 (m-80) cc_final: 0.8394 (m-80) REVERT: B 266 MET cc_start: 0.9171 (ppp) cc_final: 0.8650 (ppp) REVERT: B 287 TYR cc_start: 0.8671 (t80) cc_final: 0.8327 (t80) REVERT: C 65 TRP cc_start: 0.9384 (p90) cc_final: 0.9166 (p90) REVERT: C 125 LYS cc_start: 0.8287 (tttm) cc_final: 0.7944 (tmtt) REVERT: C 187 VAL cc_start: 0.9596 (t) cc_final: 0.9095 (t) REVERT: C 215 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8370 (mmmt) REVERT: C 231 LEU cc_start: 0.9104 (mt) cc_final: 0.8837 (mt) REVERT: C 252 TYR cc_start: 0.8914 (t80) cc_final: 0.8654 (t80) REVERT: C 256 LEU cc_start: 0.9116 (mm) cc_final: 0.8828 (mm) REVERT: C 269 ASP cc_start: 0.8415 (m-30) cc_final: 0.8197 (m-30) REVERT: C 287 TYR cc_start: 0.8764 (t80) cc_final: 0.8366 (t80) REVERT: C 301 MET cc_start: 0.7832 (mmm) cc_final: 0.7555 (mmm) REVERT: C 429 LEU cc_start: 0.8959 (mt) cc_final: 0.8669 (mt) REVERT: C 435 ILE cc_start: 0.8793 (pt) cc_final: 0.8505 (tp) REVERT: D 81 ASP cc_start: 0.8291 (p0) cc_final: 0.7523 (p0) REVERT: D 103 PHE cc_start: 0.8687 (m-80) cc_final: 0.8059 (m-80) REVERT: D 155 VAL cc_start: 0.9182 (p) cc_final: 0.8898 (p) REVERT: D 215 LYS cc_start: 0.8690 (tptm) cc_final: 0.8180 (mmmm) REVERT: D 227 MET cc_start: 0.8151 (ttm) cc_final: 0.7773 (tpp) REVERT: D 266 MET cc_start: 0.9258 (ptp) cc_final: 0.8845 (ptt) REVERT: D 287 TYR cc_start: 0.8924 (t80) cc_final: 0.8406 (t80) REVERT: D 425 PHE cc_start: 0.8704 (t80) cc_final: 0.7973 (t80) REVERT: D 429 LEU cc_start: 0.9072 (mt) cc_final: 0.8841 (mt) REVERT: E 125 LYS cc_start: 0.6148 (tptt) cc_final: 0.5658 (tptp) REVERT: E 151 MET cc_start: 0.8362 (ttp) cc_final: 0.8086 (ttp) REVERT: E 196 GLN cc_start: 0.9108 (tp40) cc_final: 0.8676 (tp40) REVERT: E 215 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8106 (mmmm) REVERT: E 238 LEU cc_start: 0.8880 (mp) cc_final: 0.8509 (mp) REVERT: E 252 TYR cc_start: 0.8909 (t80) cc_final: 0.8559 (t80) REVERT: E 256 LEU cc_start: 0.9056 (mm) cc_final: 0.8829 (mm) REVERT: E 287 TYR cc_start: 0.8810 (t80) cc_final: 0.8522 (t80) REVERT: E 291 MET cc_start: 0.9225 (mmt) cc_final: 0.8797 (mmt) REVERT: E 296 LEU cc_start: 0.9373 (mt) cc_final: 0.9148 (mt) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.0702 time to fit residues: 46.5700 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 : 0.466 ------------------------------------------------------------------------------- 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: 2.9990 chunk 118 optimal weight: 0.0570 chunk 72 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN B 40 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.103102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.081674 restraints weight = 38119.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084295 restraints weight = 25146.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086226 restraints weight = 18605.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.087511 restraints weight = 14901.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088521 restraints weight = 12731.912| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3169 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= 0.168 Angle : 0.735 12.128 17655 Z= 0.362 Chirality : 0.047 0.266 2167 Planarity : 0.004 0.032 2122 Dihedral : 4.387 20.894 1771 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.27 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.52 % 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 are not related in a simple way. whole: -0.54 (0.21), residues: 1610 helix: 1.21 (0.22), residues: 525 sheet: -0.81 (0.26), residues: 440 loop : -1.27 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.030 0.002 TYR A 252 PHE 0.043 0.002 PHE D 289 TRP 0.018 0.002 TRP B 77 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (12848) covalent geometry : angle 0.73039 / 0.36 (17633) SS BOND : bond 0.00201 / 0.10 ( 5) SS BOND : angle 1.98599 / 1.27 ( 10) hydrogen bonds : bond 0.04032 / 2.74 ( 589) hydrogen bonds : angle 4.69225 / 3.33 ( 1665) link_NAG-ASN : bond 0.00521 / 0.26 ( 4) link_NAG-ASN : angle 2.59740 / 1.46 ( 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 414 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 412 time to evaluate : 0.337 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 125 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8673 (tttm) REVERT: A 127 MET cc_start: 0.7460 (ttt) cc_final: 0.7067 (ttt) REVERT: A 234 PHE cc_start: 0.9041 (t80) cc_final: 0.8829 (t80) REVERT: A 265 MET cc_start: 0.8697 (ttt) cc_final: 0.8335 (ttm) REVERT: B 103 PHE cc_start: 0.8970 (m-80) cc_final: 0.8384 (m-80) REVERT: B 225 PHE cc_start: 0.8637 (m-80) cc_final: 0.8360 (m-80) REVERT: B 266 MET cc_start: 0.9003 (ppp) cc_final: 0.8483 (ppp) REVERT: B 268 SER cc_start: 0.9282 (p) cc_final: 0.9039 (p) REVERT: B 287 TYR cc_start: 0.8671 (t80) cc_final: 0.8330 (t80) REVERT: C 65 TRP cc_start: 0.9387 (p90) cc_final: 0.9121 (p90) REVERT: C 77 TRP cc_start: 0.7115 (p-90) cc_final: 0.6891 (p-90) REVERT: C 125 LYS cc_start: 0.8251 (tttm) cc_final: 0.7927 (tmtt) REVERT: C 231 LEU cc_start: 0.9113 (mt) cc_final: 0.8806 (mt) REVERT: C 252 TYR cc_start: 0.8840 (t80) cc_final: 0.8618 (t80) REVERT: C 256 LEU cc_start: 0.9020 (mm) cc_final: 0.8769 (mm) REVERT: C 287 TYR cc_start: 0.8727 (t80) cc_final: 0.8289 (t80) REVERT: C 429 LEU cc_start: 0.9024 (mt) cc_final: 0.8728 (mt) REVERT: C 435 ILE cc_start: 0.8937 (pt) cc_final: 0.8664 (tt) REVERT: D 81 ASP cc_start: 0.8298 (p0) cc_final: 0.7549 (p0) REVERT: D 103 PHE cc_start: 0.8656 (m-80) cc_final: 0.8012 (m-80) REVERT: D 155 VAL cc_start: 0.9037 (p) cc_final: 0.8813 (p) REVERT: D 215 LYS cc_start: 0.8766 (tptm) cc_final: 0.8243 (mmmm) REVERT: D 227 MET cc_start: 0.8155 (ttm) cc_final: 0.7724 (tpp) REVERT: D 287 TYR cc_start: 0.8911 (t80) cc_final: 0.8353 (t80) REVERT: D 425 PHE cc_start: 0.8745 (t80) cc_final: 0.8507 (t80) REVERT: D 429 LEU cc_start: 0.9171 (mt) cc_final: 0.8883 (mt) REVERT: E 125 LYS cc_start: 0.6342 (tptt) cc_final: 0.5705 (tptp) REVERT: E 151 MET cc_start: 0.8374 (ttp) cc_final: 0.8130 (ttp) REVERT: E 196 GLN cc_start: 0.9107 (tp40) cc_final: 0.8693 (tp40) REVERT: E 215 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8114 (mmmm) REVERT: E 235 LEU cc_start: 0.9525 (mm) cc_final: 0.8642 (tp) REVERT: E 238 LEU cc_start: 0.8932 (mp) cc_final: 0.8662 (mp) REVERT: E 252 TYR cc_start: 0.8927 (t80) cc_final: 0.8426 (t80) REVERT: E 256 LEU cc_start: 0.9035 (mm) cc_final: 0.8783 (mm) REVERT: E 287 TYR cc_start: 0.8732 (t80) cc_final: 0.8422 (t80) REVERT: E 291 MET cc_start: 0.9166 (mmt) cc_final: 0.8739 (mmt) REVERT: E 296 LEU cc_start: 0.9370 (mt) cc_final: 0.9139 (mt) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.0655 time to fit residues: 43.6069 Evaluate side-chains 355 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 38 optimal weight: 0.0670 chunk 94 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 chunk 125 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN B 40 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3586 r_free = 0.3586 target = 0.101663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080596 restraints weight = 38431.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083114 restraints weight = 25085.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084971 restraints weight = 18563.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.086319 restraints weight = 14917.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087137 restraints weight = 12651.806| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12857 Z= 0.188 Angle : 0.741 12.209 17655 Z= 0.367 Chirality : 0.048 0.273 2167 Planarity : 0.004 0.031 2122 Dihedral : 4.475 20.988 1771 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 0.08 % Allowed : 0.63 % Favored : 99.29 % 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 are not related in a simple way. whole: -0.57 (0.21), residues: 1610 helix: 1.18 (0.22), residues: 525 sheet: -0.83 (0.26), residues: 440 loop : -1.29 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 216 TYR 0.030 0.002 TYR E 67 PHE 0.035 0.002 PHE A 289 TRP 0.022 0.002 TRP A 128 HIS 0.005 0.001 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (12848) covalent geometry : angle 0.73703 / 0.37 (17633) SS BOND : bond 0.00215 / 0.11 ( 5) SS BOND : angle 2.02178 / 1.29 ( 10) hydrogen bonds : bond 0.04050 / 2.79 ( 589) hydrogen bonds : angle 4.74084 / 3.36 ( 1665) link_NAG-ASN : bond 0.00477 / 0.24 ( 4) link_NAG-ASN : angle 2.57807 / 1.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.46 seconds wall clock time: 33 minutes 35.40 seconds (2015.40 seconds total)