Starting phenix.real_space_refine on Wed Jun 11 08:55:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bx5_16308/06_2025/8bx5_16308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bx5_16308/06_2025/8bx5_16308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bx5_16308/06_2025/8bx5_16308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bx5_16308/06_2025/8bx5_16308.map" model { file = "/net/cci-nas-00/data/ceres_data/8bx5_16308/06_2025/8bx5_16308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bx5_16308/06_2025/8bx5_16308.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 11} 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: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 11} 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: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} 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: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} 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: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.63, per 1000 atoms: 0.69 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: 3.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.32 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: 3.41 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3345 1.33 - 1.45: 2459 1.45 - 1.58: 6913 1.58 - 1.70: 0 1.70 - 1.82: 131 Bond restraints: 12848 Sorted by residual: bond pdb=" N VAL B 166 " pdb=" CA VAL B 166 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.23e-02 6.61e+03 1.45e+01 bond pdb=" N VAL A 168 " pdb=" CA VAL A 168 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.37e+01 bond pdb=" N VAL D 166 " pdb=" CA VAL D 166 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N VAL C 166 " pdb=" CA VAL C 166 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N VAL E 168 " pdb=" CA VAL E 168 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 ... (remaining 12843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16997 1.81 - 3.61: 480 3.61 - 5.42: 114 5.42 - 7.22: 32 7.22 - 9.03: 10 Bond angle restraints: 17633 Sorted by residual: angle pdb=" N VAL A 166 " pdb=" CA VAL A 166 " pdb=" CB VAL A 166 " ideal model delta sigma weight residual 112.45 104.38 8.07 1.12e+00 7.97e-01 5.20e+01 angle pdb=" N VAL E 166 " pdb=" CA VAL E 166 " pdb=" CB VAL E 166 " ideal model delta sigma weight residual 111.23 102.20 9.03 1.65e+00 3.67e-01 2.99e+01 angle pdb=" N VAL C 166 " pdb=" CA VAL C 166 " pdb=" CB VAL C 166 " ideal model delta sigma weight residual 112.44 105.48 6.96 1.68e+00 3.54e-01 1.72e+01 angle pdb=" C MET E 265 " pdb=" N MET E 266 " pdb=" CA MET E 266 " ideal model delta sigma weight residual 121.14 114.03 7.11 1.75e+00 3.27e-01 1.65e+01 angle pdb=" CA VAL C 166 " pdb=" CB VAL C 166 " pdb=" CG1 VAL C 166 " ideal model delta sigma weight residual 110.40 117.18 -6.78 1.70e+00 3.46e-01 1.59e+01 ... (remaining 17628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.44: 6906 19.44 - 38.88: 481 38.88 - 58.31: 88 58.31 - 77.75: 12 77.75 - 97.19: 14 Dihedral angle restraints: 7501 sinusoidal: 2656 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS B 138 " pdb=" SG CYS B 138 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 35.53 57.47 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual -86.00 -29.53 -56.47 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" N VAL E 166 " pdb=" C VAL E 166 " pdb=" CA VAL E 166 " pdb=" CB VAL E 166 " ideal model delta harmonic sigma weight residual 123.40 112.50 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2142 0.146 - 0.292: 17 0.292 - 0.438: 3 0.438 - 0.584: 2 0.584 - 0.730: 3 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB VAL C 166 " pdb=" CA VAL C 166 " pdb=" CG1 VAL C 166 " pdb=" CG2 VAL C 166 " both_signs ideal model delta sigma weight residual False -2.63 -1.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 167 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2164 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.330 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG D 501 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 501 " -0.313 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C7 NAG C 501 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 501 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 501 " 0.490 2.00e-02 2.50e+03 pdb=" O7 NAG C 501 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.295 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG E 501 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.440 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " -0.045 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1552 2.75 - 3.29: 13264 3.29 - 3.83: 21602 3.83 - 4.36: 23739 4.36 - 4.90: 39905 Nonbonded interactions: 100062 Sorted by model distance: nonbonded pdb=" OG1 THR E 123 " pdb=" NZ LYS E 125 " model vdw 2.218 3.120 nonbonded pdb=" O ILE C 242 " pdb=" NH1 ARG C 249 " model vdw 2.247 3.120 nonbonded pdb=" O HOH A 601 " pdb=" O HOH B 501 " model vdw 2.257 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OH TYR B 220 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN C 34 " pdb=" OG SER C 36 " model vdw 2.260 3.040 ... (remaining 100057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 126 or (resid 127 and \ (name N or name CA or name C or name O or name CB )) or resid 128 through 304 o \ r (resid 305 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 06 through 422 or (resid 423 through 424 and (name N or name CA or name C or nam \ e O or name CB )) or resid 425 through 443)) selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 126 or (resid 127 and \ (name N or name CA or name C or name O or name CB )) or resid 128 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE )) or resid 271 through 306 or (resid 307 and (name N or nam \ e CA or name C or name O or name CB )) or resid 414 through 422 or (resid 423 th \ rough 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 443)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 126 or (resid 127 and (name N or n \ ame CA or name C or name O or name CB )) or resid 128 through 443)) selection = (chain 'D' and (resid 12 through 422 or (resid 423 through 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 through 443)) selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 126 or (resid 127 and (name N or n \ ame CA or name C or name O or name CB )) or resid 128 through 422 or (resid 423 \ through 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 443)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.860 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12857 Z= 0.186 Angle : 0.805 12.662 17655 Z= 0.413 Chirality : 0.059 0.730 2167 Planarity : 0.012 0.288 2122 Dihedral : 14.220 97.188 4356 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.63 % Allowed : 0.16 % Favored : 99.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.002 TRP D 159 HIS 0.004 0.001 HIS E 131 PHE 0.035 0.002 PHE A 289 TYR 0.028 0.002 TYR E 252 ARG 0.004 0.000 ARG A 216 Details of bonding type rmsd link_NAG-ASN : bond 0.01897 ( 4) link_NAG-ASN : angle 6.84784 ( 12) hydrogen bonds : bond 0.11792 ( 589) hydrogen bonds : angle 5.37505 ( 1665) SS BOND : bond 0.00247 ( 5) SS BOND : angle 1.89906 ( 10) covalent geometry : bond 0.00347 (12848) covalent geometry : angle 0.78430 (17633) *********************** 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 : 1.321 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: 0.6475 (t60) REVERT: A 161 HIS cc_start: 0.7680 (p90) cc_final: 0.7129 (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: 0.5777 (tpt) REVERT: B 227 MET cc_start: 0.8115 (ttm) cc_final: 0.7109 (tpp) REVERT: B 256 LEU cc_start: 0.9370 (mm) cc_final: 0.9169 (mm) REVERT: B 287 TYR cc_start: 0.8743 (t80) cc_final: 0.8322 (t80) REVERT: B 301 MET cc_start: 0.8903 (mmp) cc_final: 0.8323 (ptm) REVERT: C 62 THR cc_start: 0.9011 (p) cc_final: 0.8791 (p) REVERT: C 151 MET cc_start: 0.7088 (ttp) cc_final: 0.6859 (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: 0.8641 (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: 0.8701 (mmm) 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: 0.8135 (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: 0.7677 (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: 0.8797 (tp) REVERT: E 238 LEU cc_start: 0.9094 (mp) cc_final: 0.8762 (mp) 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: 0.9146 (m-10) outliers start: 8 outliers final: 0 residues processed: 464 average time/residue: 0.1887 time to fit residues: 133.6668 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 : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 304 ASN C 196 GLN D 161 HIS E 58 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081450 restraints weight = 37650.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083881 restraints weight = 24852.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085665 restraints weight = 18549.725| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12857 Z= 0.202 Angle : 0.700 12.138 17655 Z= 0.347 Chirality : 0.047 0.382 2167 Planarity : 0.004 0.038 2122 Dihedral : 6.597 49.053 1855 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1610 helix: 1.29 (0.22), residues: 525 sheet: -1.13 (0.25), residues: 425 loop : -1.30 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 65 HIS 0.008 0.001 HIS D 131 PHE 0.034 0.002 PHE C 428 TYR 0.028 0.002 TYR D 252 ARG 0.007 0.001 ARG A 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 4) link_NAG-ASN : angle 3.50617 ( 12) hydrogen bonds : bond 0.04192 ( 589) hydrogen bonds : angle 4.87875 ( 1665) SS BOND : bond 0.00176 ( 5) SS BOND : angle 2.07830 ( 10) covalent geometry : bond 0.00434 (12848) covalent geometry : angle 0.69310 (17633) *********************** 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 413 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 1.378 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 125 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8147 (tttm) REVERT: A 173 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8125 (tp-100) REVERT: A 215 LYS cc_start: 0.8222 (mmmt) cc_final: 0.8022 (mmmt) REVERT: A 234 PHE cc_start: 0.8933 (t80) cc_final: 0.8623 (t80) REVERT: A 287 TYR cc_start: 0.8570 (t80) cc_final: 0.8250 (t80) REVERT: A 296 LEU cc_start: 0.9171 (mt) cc_final: 0.8912 (mt) REVERT: B 103 PHE cc_start: 0.9061 (m-10) cc_final: 0.8806 (m-80) REVERT: B 125 LYS cc_start: 0.8467 (tttp) cc_final: 0.8239 (tttm) REVERT: B 227 MET cc_start: 0.8549 (ttm) cc_final: 0.8321 (ttm) REVERT: B 266 MET cc_start: 0.9041 (ppp) cc_final: 0.8746 (ppp) REVERT: B 269 ASP cc_start: 0.7714 (m-30) cc_final: 0.7460 (m-30) REVERT: C 151 MET cc_start: 0.8313 (ttp) cc_final: 0.8074 (ttm) REVERT: C 215 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8430 (mmmt) REVERT: C 231 LEU cc_start: 0.9035 (mt) cc_final: 0.8798 (mt) REVERT: C 287 TYR cc_start: 0.8644 (t80) cc_final: 0.8155 (t80) REVERT: C 429 LEU cc_start: 0.8915 (mt) cc_final: 0.8664 (mt) REVERT: C 435 ILE cc_start: 0.8802 (pt) cc_final: 0.8446 (tp) REVERT: D 103 PHE cc_start: 0.8527 (m-80) cc_final: 0.8000 (m-80) REVERT: D 252 TYR cc_start: 0.8850 (t80) cc_final: 0.8529 (t80) REVERT: D 265 MET cc_start: 0.8519 (ttp) cc_final: 0.8275 (ttp) REVERT: D 287 TYR cc_start: 0.8865 (t80) cc_final: 0.8393 (t80) REVERT: D 425 PHE cc_start: 0.8470 (t80) cc_final: 0.8240 (t80) REVERT: D 429 LEU cc_start: 0.9155 (mt) cc_final: 0.8939 (mt) REVERT: E 62 THR cc_start: 0.9187 (p) cc_final: 0.8908 (p) REVERT: E 74 GLN cc_start: 0.8399 (mp10) cc_final: 0.8184 (mp10) REVERT: E 151 MET cc_start: 0.8652 (ttp) cc_final: 0.8383 (ttp) REVERT: E 215 LYS cc_start: 0.8395 (mmmm) cc_final: 0.7903 (mmmm) REVERT: E 225 PHE cc_start: 0.8691 (m-80) cc_final: 0.8268 (m-80) REVERT: E 227 MET cc_start: 0.8395 (ttm) cc_final: 0.8062 (ttm) REVERT: E 234 PHE cc_start: 0.8649 (t80) cc_final: 0.8400 (t80) REVERT: E 235 LEU cc_start: 0.9540 (mt) cc_final: 0.9185 (mt) REVERT: E 238 LEU cc_start: 0.8921 (mp) cc_final: 0.8665 (mp) REVERT: E 287 TYR cc_start: 0.8606 (t80) cc_final: 0.8347 (t80) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.1811 time to fit residues: 115.9987 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 : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081676 restraints weight = 37485.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084206 restraints weight = 24730.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085951 restraints weight = 18390.318| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12857 Z= 0.172 Angle : 0.670 11.362 17655 Z= 0.336 Chirality : 0.045 0.270 2167 Planarity : 0.003 0.031 2122 Dihedral : 5.937 57.110 1855 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1610 helix: 1.28 (0.22), residues: 525 sheet: -1.05 (0.26), residues: 410 loop : -1.24 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 185 HIS 0.004 0.001 HIS A 68 PHE 0.034 0.002 PHE D 289 TYR 0.020 0.002 TYR B 223 ARG 0.004 0.000 ARG B 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 4) link_NAG-ASN : angle 2.42567 ( 12) hydrogen bonds : bond 0.04044 ( 589) hydrogen bonds : angle 4.82611 ( 1665) SS BOND : bond 0.01041 ( 5) SS BOND : angle 1.89958 ( 10) covalent geometry : bond 0.00369 (12848) covalent geometry : angle 0.66598 (17633) *********************** 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 426 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 1.505 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: 0.9574 (tp) cc_final: 0.9321 (mm) REVERT: A 173 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8088 (tp-100) REVERT: A 241 PHE cc_start: 0.8650 (m-80) cc_final: 0.8375 (m-10) REVERT: A 287 TYR cc_start: 0.8393 (t80) cc_final: 0.7866 (t80) REVERT: A 296 LEU cc_start: 0.9080 (mt) cc_final: 0.8733 (mt) REVERT: B 72 ASP cc_start: 0.8712 (t70) cc_final: 0.8352 (t0) REVERT: B 103 PHE cc_start: 0.9177 (m-10) cc_final: 0.8711 (m-80) REVERT: B 266 MET cc_start: 0.8966 (ppp) cc_final: 0.8601 (ppp) REVERT: B 268 SER cc_start: 0.9297 (p) cc_final: 0.8996 (t) REVERT: B 269 ASP cc_start: 0.7671 (m-30) cc_final: 0.7464 (m-30) REVERT: B 291 MET cc_start: 0.9007 (tpp) cc_final: 0.8455 (mmm) REVERT: B 298 PHE cc_start: 0.9271 (m-10) cc_final: 0.8225 (m-10) REVERT: B 429 LEU cc_start: 0.9114 (pp) cc_final: 0.8829 (pp) REVERT: C 151 MET cc_start: 0.8488 (ttp) cc_final: 0.8212 (ttm) REVERT: C 269 ASP cc_start: 0.8439 (m-30) cc_final: 0.8209 (m-30) REVERT: C 287 TYR cc_start: 0.8610 (t80) cc_final: 0.8139 (t80) REVERT: C 429 LEU cc_start: 0.8878 (mt) cc_final: 0.8645 (mt) REVERT: C 435 ILE cc_start: 0.8857 (pt) cc_final: 0.8416 (tp) REVERT: D 62 THR cc_start: 0.8878 (p) cc_final: 0.8524 (t) REVERT: D 252 TYR cc_start: 0.8842 (t80) cc_final: 0.8583 (t80) REVERT: D 265 MET cc_start: 0.8550 (ttp) cc_final: 0.8286 (ttp) REVERT: D 287 TYR cc_start: 0.8775 (t80) cc_final: 0.8404 (t80) REVERT: D 289 PHE cc_start: 0.8989 (t80) cc_final: 0.8446 (t80) REVERT: D 425 PHE cc_start: 0.8553 (t80) cc_final: 0.8176 (t80) REVERT: D 429 LEU cc_start: 0.9180 (mt) cc_final: 0.8899 (mt) REVERT: E 62 THR cc_start: 0.9240 (p) cc_final: 0.8817 (t) REVERT: E 74 GLN cc_start: 0.8398 (mp10) cc_final: 0.8177 (mp10) REVERT: E 151 MET cc_start: 0.8664 (ttp) cc_final: 0.8375 (ttp) REVERT: E 196 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8713 (tp40) REVERT: E 215 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8253 (mmmm) REVERT: E 225 PHE cc_start: 0.8664 (m-80) cc_final: 0.8208 (m-80) REVERT: E 227 MET cc_start: 0.8264 (ttm) cc_final: 0.8063 (ttm) REVERT: E 235 LEU cc_start: 0.9460 (mt) cc_final: 0.8914 (mm) REVERT: E 238 LEU cc_start: 0.8839 (mp) cc_final: 0.8528 (mp) REVERT: E 252 TYR cc_start: 0.8845 (t80) cc_final: 0.8373 (t80) REVERT: E 256 LEU cc_start: 0.8792 (mm) cc_final: 0.8547 (mm) REVERT: E 287 TYR cc_start: 0.8696 (t80) cc_final: 0.8494 (t80) REVERT: E 291 MET cc_start: 0.9012 (mmt) cc_final: 0.8676 (mmt) outliers start: 1 outliers final: 0 residues processed: 425 average time/residue: 0.1790 time to fit residues: 120.2563 Evaluate side-chains 363 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083466 restraints weight = 36621.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086044 restraints weight = 24433.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087856 restraints weight = 18239.287| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12857 Z= 0.127 Angle : 0.660 9.388 17655 Z= 0.326 Chirality : 0.045 0.230 2167 Planarity : 0.003 0.031 2122 Dihedral : 5.530 54.173 1855 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.98 % Favored : 96.89 % Rotamer: Outliers : 0.08 % Allowed : 5.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1610 helix: 1.21 (0.22), residues: 525 sheet: -0.92 (0.26), residues: 425 loop : -1.31 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 65 HIS 0.003 0.001 HIS C 161 PHE 0.026 0.002 PHE D 289 TYR 0.016 0.001 TYR E 223 ARG 0.003 0.000 ARG B 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00827 ( 4) link_NAG-ASN : angle 2.43144 ( 12) hydrogen bonds : bond 0.03860 ( 589) hydrogen bonds : angle 4.68994 ( 1665) SS BOND : bond 0.00111 ( 5) SS BOND : angle 2.02647 ( 10) covalent geometry : bond 0.00278 (12848) covalent geometry : angle 0.65566 (17633) *********************** 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 437 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8314 (ttpp) REVERT: A 173 GLN cc_start: 0.8351 (tp-100) cc_final: 0.8061 (tp-100) REVERT: A 234 PHE cc_start: 0.8953 (t80) cc_final: 0.8689 (t80) REVERT: A 265 MET cc_start: 0.9110 (ttm) cc_final: 0.8565 (ttt) REVERT: A 287 TYR cc_start: 0.8442 (t80) cc_final: 0.7868 (t80) REVERT: A 296 LEU cc_start: 0.9047 (mt) cc_final: 0.8706 (mt) REVERT: A 429 LEU cc_start: 0.9113 (pp) cc_final: 0.8870 (pp) REVERT: B 72 ASP cc_start: 0.8675 (t70) cc_final: 0.8338 (t0) REVERT: B 103 PHE cc_start: 0.9157 (m-10) cc_final: 0.8533 (m-80) REVERT: B 265 MET cc_start: 0.8003 (ttt) cc_final: 0.7799 (ttp) REVERT: B 266 MET cc_start: 0.8897 (ppp) cc_final: 0.8465 (ppp) REVERT: B 268 SER cc_start: 0.9249 (p) cc_final: 0.8878 (t) REVERT: B 269 ASP cc_start: 0.7617 (m-30) cc_final: 0.7340 (m-30) REVERT: B 429 LEU cc_start: 0.9106 (pp) cc_final: 0.8840 (pp) REVERT: C 65 TRP cc_start: 0.9284 (p90) cc_final: 0.8945 (p90) REVERT: C 151 MET cc_start: 0.8387 (ttp) cc_final: 0.8148 (ttp) REVERT: C 287 TYR cc_start: 0.8575 (t80) cc_final: 0.8133 (t80) REVERT: C 429 LEU cc_start: 0.8950 (mt) cc_final: 0.8648 (mt) REVERT: C 435 ILE cc_start: 0.8807 (pt) cc_final: 0.8503 (tp) REVERT: D 65 TRP cc_start: 0.9338 (p90) cc_final: 0.9018 (p90) REVERT: D 103 PHE cc_start: 0.8662 (m-80) cc_final: 0.8139 (m-80) REVERT: D 227 MET cc_start: 0.8562 (ttm) cc_final: 0.8291 (ttm) REVERT: D 287 TYR cc_start: 0.8761 (t80) cc_final: 0.8374 (t80) REVERT: D 289 PHE cc_start: 0.9138 (t80) cc_final: 0.8488 (t80) REVERT: D 425 PHE cc_start: 0.8494 (t80) cc_final: 0.8146 (t80) REVERT: D 429 LEU cc_start: 0.9145 (mt) cc_final: 0.8904 (mt) REVERT: E 62 THR cc_start: 0.9175 (p) cc_final: 0.8940 (p) REVERT: E 151 MET cc_start: 0.8345 (ttp) cc_final: 0.8053 (ttp) REVERT: E 196 GLN cc_start: 0.9077 (tp40) cc_final: 0.8606 (tp40) REVERT: E 215 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8148 (mmmm) REVERT: E 225 PHE cc_start: 0.8661 (m-80) cc_final: 0.8182 (m-80) REVERT: E 235 LEU cc_start: 0.9427 (mt) cc_final: 0.8849 (mm) REVERT: E 238 LEU cc_start: 0.8852 (mp) cc_final: 0.8573 (mp) REVERT: E 252 TYR cc_start: 0.8899 (t80) cc_final: 0.8305 (t80) REVERT: E 287 TYR cc_start: 0.8754 (t80) cc_final: 0.8538 (t80) REVERT: E 291 MET cc_start: 0.8978 (mmt) cc_final: 0.8567 (mmt) REVERT: E 296 LEU cc_start: 0.9291 (mt) cc_final: 0.9070 (mt) outliers start: 1 outliers final: 0 residues processed: 436 average time/residue: 0.1882 time to fit residues: 129.9958 Evaluate side-chains 361 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 143 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083296 restraints weight = 36616.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085895 restraints weight = 24152.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087685 restraints weight = 17884.730| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12857 Z= 0.133 Angle : 0.675 10.668 17655 Z= 0.330 Chirality : 0.046 0.217 2167 Planarity : 0.003 0.031 2122 Dihedral : 5.344 54.312 1855 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.35 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1610 helix: 1.17 (0.22), residues: 525 sheet: -0.92 (0.26), residues: 430 loop : -1.24 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 159 HIS 0.005 0.001 HIS C 161 PHE 0.032 0.002 PHE A 425 TYR 0.014 0.001 TYR E 67 ARG 0.003 0.000 ARG B 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 4) link_NAG-ASN : angle 2.29371 ( 12) hydrogen bonds : bond 0.03809 ( 589) hydrogen bonds : angle 4.67583 ( 1665) SS BOND : bond 0.00175 ( 5) SS BOND : angle 2.07587 ( 10) covalent geometry : bond 0.00296 (12848) covalent geometry : angle 0.67115 (17633) *********************** 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 421 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.401 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: 0.8877 (mmmt) cc_final: 0.8395 (tttt) REVERT: A 173 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7976 (tp-100) REVERT: A 234 PHE cc_start: 0.8939 (t80) cc_final: 0.8685 (t80) REVERT: A 241 PHE cc_start: 0.8509 (m-80) cc_final: 0.8268 (m-10) REVERT: A 265 MET cc_start: 0.9143 (ttm) cc_final: 0.8655 (ttt) REVERT: A 287 TYR cc_start: 0.8416 (t80) cc_final: 0.7834 (t80) REVERT: A 296 LEU cc_start: 0.9065 (mt) cc_final: 0.8753 (mt) REVERT: B 72 ASP cc_start: 0.8680 (t70) cc_final: 0.8350 (t0) REVERT: B 256 LEU cc_start: 0.8936 (mm) cc_final: 0.8667 (mm) REVERT: B 265 MET cc_start: 0.8210 (ttt) cc_final: 0.7619 (ttp) REVERT: B 266 MET cc_start: 0.9063 (ppp) cc_final: 0.8694 (ppp) REVERT: B 268 SER cc_start: 0.9246 (p) cc_final: 0.8913 (t) REVERT: B 269 ASP cc_start: 0.7616 (m-30) cc_final: 0.7375 (m-30) REVERT: B 287 TYR cc_start: 0.8618 (t80) cc_final: 0.8359 (t80) REVERT: B 291 MET cc_start: 0.9059 (tpp) cc_final: 0.8269 (mmm) REVERT: C 65 TRP cc_start: 0.9308 (p90) cc_final: 0.9064 (p90) REVERT: C 151 MET cc_start: 0.8456 (ttp) cc_final: 0.8242 (ttp) REVERT: C 187 VAL cc_start: 0.9569 (t) cc_final: 0.9211 (t) REVERT: C 266 MET cc_start: 0.9173 (ptp) cc_final: 0.8960 (ptm) REVERT: C 287 TYR cc_start: 0.8573 (t80) cc_final: 0.8205 (t80) REVERT: C 429 LEU cc_start: 0.9013 (mt) cc_final: 0.8682 (mt) REVERT: C 435 ILE cc_start: 0.8759 (pt) cc_final: 0.8434 (tp) REVERT: D 65 TRP cc_start: 0.9258 (p90) cc_final: 0.8967 (p90) REVERT: D 103 PHE cc_start: 0.8590 (m-80) cc_final: 0.7871 (m-80) REVERT: D 287 TYR cc_start: 0.8767 (t80) cc_final: 0.8358 (t80) REVERT: D 425 PHE cc_start: 0.8533 (t80) cc_final: 0.8252 (t80) REVERT: D 429 LEU cc_start: 0.9087 (mt) cc_final: 0.8860 (mt) REVERT: E 151 MET cc_start: 0.8414 (ttp) cc_final: 0.8080 (ttp) REVERT: E 196 GLN cc_start: 0.9088 (tp40) cc_final: 0.8731 (tp40) REVERT: E 215 LYS cc_start: 0.8447 (mmmm) cc_final: 0.8138 (mmmm) REVERT: E 225 PHE cc_start: 0.8575 (m-80) cc_final: 0.8031 (m-80) REVERT: E 227 MET cc_start: 0.8341 (ttm) cc_final: 0.8048 (ttm) REVERT: E 235 LEU cc_start: 0.9475 (mt) cc_final: 0.8913 (mm) REVERT: E 238 LEU cc_start: 0.8870 (mp) cc_final: 0.8616 (mp) REVERT: E 252 TYR cc_start: 0.8897 (t80) cc_final: 0.8484 (t80) REVERT: E 291 MET cc_start: 0.9099 (mmt) cc_final: 0.8731 (mmt) REVERT: E 296 LEU cc_start: 0.9251 (mt) cc_final: 0.9045 (mt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1793 time to fit residues: 118.6268 Evaluate side-chains 365 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 14 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.104185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082595 restraints weight = 36972.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085139 restraints weight = 24637.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086974 restraints weight = 18391.851| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12857 Z= 0.141 Angle : 0.662 9.629 17655 Z= 0.329 Chirality : 0.045 0.199 2167 Planarity : 0.003 0.032 2122 Dihedral : 5.270 54.172 1855 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1610 helix: 1.17 (0.22), residues: 525 sheet: -0.67 (0.27), residues: 400 loop : -1.18 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 65 HIS 0.004 0.001 HIS C 161 PHE 0.024 0.002 PHE A 425 TYR 0.020 0.001 TYR E 122 ARG 0.003 0.000 ARG B 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 4) link_NAG-ASN : angle 2.26124 ( 12) hydrogen bonds : bond 0.03828 ( 589) hydrogen bonds : angle 4.62307 ( 1665) SS BOND : bond 0.00652 ( 5) SS BOND : angle 2.09525 ( 10) covalent geometry : bond 0.00314 (12848) covalent geometry : angle 0.65772 (17633) *********************** 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 419 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9452 (tp) cc_final: 0.9224 (mm) REVERT: A 103 PHE cc_start: 0.9186 (m-10) cc_final: 0.8872 (m-80) REVERT: A 125 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8409 (tttt) REVERT: A 173 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7958 (tp-100) REVERT: A 234 PHE cc_start: 0.8943 (t80) cc_final: 0.8705 (t80) REVERT: A 265 MET cc_start: 0.9281 (ttm) cc_final: 0.8691 (ttt) REVERT: A 287 TYR cc_start: 0.8389 (t80) cc_final: 0.7917 (t80) REVERT: B 72 ASP cc_start: 0.8691 (t70) cc_final: 0.8317 (t0) REVERT: B 265 MET cc_start: 0.8440 (ttt) cc_final: 0.7902 (ttp) REVERT: B 266 MET cc_start: 0.9056 (ppp) cc_final: 0.8707 (ppp) REVERT: B 268 SER cc_start: 0.9256 (p) cc_final: 0.8910 (t) REVERT: B 269 ASP cc_start: 0.7699 (m-30) cc_final: 0.7430 (m-30) REVERT: B 287 TYR cc_start: 0.8607 (t80) cc_final: 0.8349 (t80) REVERT: B 291 MET cc_start: 0.9058 (tpp) cc_final: 0.8477 (mmm) REVERT: C 151 MET cc_start: 0.8497 (ttp) cc_final: 0.8117 (ttp) REVERT: C 287 TYR cc_start: 0.8656 (t80) cc_final: 0.8219 (t80) REVERT: C 429 LEU cc_start: 0.9035 (mt) cc_final: 0.8708 (mt) REVERT: C 435 ILE cc_start: 0.8790 (pt) cc_final: 0.8451 (tp) REVERT: D 65 TRP cc_start: 0.9308 (p90) cc_final: 0.9019 (p90) REVERT: D 103 PHE cc_start: 0.8588 (m-80) cc_final: 0.7764 (m-80) REVERT: D 227 MET cc_start: 0.8440 (ttm) cc_final: 0.8159 (ttm) REVERT: D 266 MET cc_start: 0.9143 (ptt) cc_final: 0.8713 (ptp) REVERT: D 287 TYR cc_start: 0.8788 (t80) cc_final: 0.8365 (t80) REVERT: D 425 PHE cc_start: 0.8602 (t80) cc_final: 0.8336 (t80) REVERT: D 429 LEU cc_start: 0.9083 (mt) cc_final: 0.8787 (mt) REVERT: E 62 THR cc_start: 0.9187 (p) cc_final: 0.8957 (p) REVERT: E 151 MET cc_start: 0.8401 (ttp) cc_final: 0.8128 (ttp) REVERT: E 196 GLN cc_start: 0.9132 (tp40) cc_final: 0.8758 (tp40) REVERT: E 215 LYS cc_start: 0.8447 (mmmm) cc_final: 0.8128 (mmmm) REVERT: E 225 PHE cc_start: 0.8660 (m-80) cc_final: 0.8322 (m-80) REVERT: E 238 LEU cc_start: 0.8801 (mp) cc_final: 0.8543 (mp) REVERT: E 287 TYR cc_start: 0.8901 (t80) cc_final: 0.8616 (t80) REVERT: E 291 MET cc_start: 0.9032 (mmt) cc_final: 0.8626 (mmt) REVERT: E 296 LEU cc_start: 0.9296 (mt) cc_final: 0.9077 (mt) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.1798 time to fit residues: 118.6275 Evaluate side-chains 374 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 38 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084360 restraints weight = 36384.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.086971 restraints weight = 23992.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088853 restraints weight = 17790.755| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12857 Z= 0.126 Angle : 0.709 14.437 17655 Z= 0.342 Chirality : 0.047 0.199 2167 Planarity : 0.003 0.032 2122 Dihedral : 5.280 55.057 1855 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1610 helix: 1.11 (0.22), residues: 525 sheet: -0.79 (0.26), residues: 430 loop : -1.24 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 65 HIS 0.004 0.001 HIS C 161 PHE 0.028 0.002 PHE A 289 TYR 0.034 0.001 TYR D 252 ARG 0.003 0.000 ARG B 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 4) link_NAG-ASN : angle 2.18077 ( 12) hydrogen bonds : bond 0.03853 ( 589) hydrogen bonds : angle 4.58687 ( 1665) SS BOND : bond 0.00186 ( 5) SS BOND : angle 2.07574 ( 10) covalent geometry : bond 0.00279 (12848) covalent geometry : angle 0.70530 (17633) *********************** 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 439 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9501 (tp) cc_final: 0.9270 (mm) REVERT: A 125 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8389 (tttt) REVERT: A 155 VAL cc_start: 0.9134 (p) cc_final: 0.8894 (p) REVERT: A 173 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7964 (tp-100) REVERT: A 234 PHE cc_start: 0.8775 (t80) cc_final: 0.8562 (t80) REVERT: A 265 MET cc_start: 0.9277 (ttm) cc_final: 0.8607 (ttt) REVERT: A 287 TYR cc_start: 0.8412 (t80) cc_final: 0.7970 (t80) REVERT: A 429 LEU cc_start: 0.9122 (pp) cc_final: 0.8901 (pp) REVERT: B 72 ASP cc_start: 0.8651 (t70) cc_final: 0.8344 (t0) REVERT: B 85 LEU cc_start: 0.9093 (tp) cc_final: 0.8770 (pp) REVERT: B 103 PHE cc_start: 0.9195 (m-10) cc_final: 0.8717 (m-80) REVERT: B 225 PHE cc_start: 0.8466 (m-80) cc_final: 0.8265 (m-80) REVERT: B 227 MET cc_start: 0.8464 (ttm) cc_final: 0.7715 (tpp) REVERT: B 265 MET cc_start: 0.8431 (ttt) cc_final: 0.7873 (ttp) REVERT: B 266 MET cc_start: 0.9000 (ppp) cc_final: 0.8608 (ppp) REVERT: B 269 ASP cc_start: 0.7659 (m-30) cc_final: 0.7389 (m-30) REVERT: B 287 TYR cc_start: 0.8583 (t80) cc_final: 0.8268 (t80) REVERT: B 291 MET cc_start: 0.9071 (tpp) cc_final: 0.8300 (mmm) REVERT: C 65 TRP cc_start: 0.9391 (p90) cc_final: 0.8971 (p90) REVERT: C 151 MET cc_start: 0.8412 (ttp) cc_final: 0.8145 (ttm) REVERT: C 187 VAL cc_start: 0.9538 (t) cc_final: 0.9274 (t) REVERT: C 256 LEU cc_start: 0.8928 (mm) cc_final: 0.8725 (mm) REVERT: C 287 TYR cc_start: 0.8602 (t80) cc_final: 0.8234 (t80) REVERT: C 429 LEU cc_start: 0.8977 (mt) cc_final: 0.8680 (mt) REVERT: C 435 ILE cc_start: 0.8706 (pt) cc_final: 0.8426 (tp) REVERT: D 65 TRP cc_start: 0.9308 (p90) cc_final: 0.9009 (p90) REVERT: D 103 PHE cc_start: 0.8540 (m-80) cc_final: 0.7826 (m-80) REVERT: D 155 VAL cc_start: 0.9123 (p) cc_final: 0.8875 (p) REVERT: D 266 MET cc_start: 0.9108 (ptt) cc_final: 0.8682 (ptp) REVERT: D 287 TYR cc_start: 0.8769 (t80) cc_final: 0.8372 (t80) REVERT: D 425 PHE cc_start: 0.8569 (t80) cc_final: 0.8312 (t80) REVERT: D 429 LEU cc_start: 0.9072 (mt) cc_final: 0.8848 (mt) REVERT: E 151 MET cc_start: 0.8407 (ttp) cc_final: 0.8149 (ttp) REVERT: E 196 GLN cc_start: 0.9090 (tp40) cc_final: 0.8691 (tp40) REVERT: E 215 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8241 (mmmm) REVERT: E 225 PHE cc_start: 0.8596 (m-80) cc_final: 0.8223 (m-80) REVERT: E 235 LEU cc_start: 0.9433 (mp) cc_final: 0.9023 (mp) REVERT: E 238 LEU cc_start: 0.8811 (mp) cc_final: 0.8520 (mp) REVERT: E 252 TYR cc_start: 0.8936 (t80) cc_final: 0.8383 (t80) REVERT: E 256 LEU cc_start: 0.8916 (mm) cc_final: 0.8498 (mm) REVERT: E 287 TYR cc_start: 0.8869 (t80) cc_final: 0.8588 (t80) REVERT: E 291 MET cc_start: 0.9162 (mmt) cc_final: 0.8724 (mmm) REVERT: E 296 LEU cc_start: 0.9277 (mt) cc_final: 0.9059 (mt) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.2018 time to fit residues: 138.7051 Evaluate side-chains 380 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3618 r_free = 0.3618 target = 0.104149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082549 restraints weight = 37180.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085119 restraints weight = 24674.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086702 restraints weight = 18329.046| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12857 Z= 0.156 Angle : 0.700 11.695 17655 Z= 0.346 Chirality : 0.046 0.217 2167 Planarity : 0.003 0.030 2122 Dihedral : 5.347 53.211 1855 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1610 helix: 1.21 (0.22), residues: 525 sheet: -0.55 (0.27), residues: 400 loop : -1.18 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 159 HIS 0.007 0.001 HIS E 131 PHE 0.033 0.002 PHE A 425 TYR 0.036 0.001 TYR D 252 ARG 0.003 0.000 ARG B 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 4) link_NAG-ASN : angle 2.17224 ( 12) hydrogen bonds : bond 0.03850 ( 589) hydrogen bonds : angle 4.57868 ( 1665) SS BOND : bond 0.00155 ( 5) SS BOND : angle 2.02072 ( 10) covalent geometry : bond 0.00354 (12848) covalent geometry : angle 0.69630 (17633) *********************** 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 418 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.386 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: 0.9502 (tp) cc_final: 0.9268 (mm) REVERT: A 125 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8573 (tttm) REVERT: A 127 MET cc_start: 0.7381 (ttt) cc_final: 0.7088 (ttt) REVERT: A 173 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8038 (tp-100) REVERT: A 215 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8090 (mmmt) REVERT: A 234 PHE cc_start: 0.8945 (t80) cc_final: 0.8683 (t80) REVERT: A 265 MET cc_start: 0.9319 (ttm) cc_final: 0.8804 (ttm) REVERT: A 287 TYR cc_start: 0.8517 (t80) cc_final: 0.8073 (t80) REVERT: A 296 LEU cc_start: 0.9179 (mt) cc_final: 0.8918 (mt) REVERT: A 425 PHE cc_start: 0.8671 (t80) cc_final: 0.8454 (t80) REVERT: B 72 ASP cc_start: 0.8690 (t70) cc_final: 0.8418 (t0) REVERT: B 225 PHE cc_start: 0.8494 (m-80) cc_final: 0.8194 (m-10) REVERT: B 265 MET cc_start: 0.8490 (ttt) cc_final: 0.7949 (ttt) REVERT: B 266 MET cc_start: 0.8957 (ppp) cc_final: 0.8697 (ppp) REVERT: B 268 SER cc_start: 0.9292 (p) cc_final: 0.9030 (p) REVERT: B 269 ASP cc_start: 0.7864 (m-30) cc_final: 0.7645 (m-30) REVERT: B 287 TYR cc_start: 0.8679 (t80) cc_final: 0.8302 (t80) REVERT: B 291 MET cc_start: 0.9054 (tpp) cc_final: 0.8350 (mmm) REVERT: C 65 TRP cc_start: 0.9409 (p90) cc_final: 0.9042 (p90) REVERT: C 69 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7225 (mm-30) REVERT: C 151 MET cc_start: 0.8376 (ttp) cc_final: 0.7829 (ttp) REVERT: C 187 VAL cc_start: 0.9536 (t) cc_final: 0.9237 (t) REVERT: C 231 LEU cc_start: 0.9088 (mt) cc_final: 0.8835 (mt) REVERT: C 256 LEU cc_start: 0.8923 (mm) cc_final: 0.8693 (mm) REVERT: C 287 TYR cc_start: 0.8710 (t80) cc_final: 0.8340 (t80) REVERT: C 429 LEU cc_start: 0.9001 (mt) cc_final: 0.8703 (mt) REVERT: C 435 ILE cc_start: 0.8783 (pt) cc_final: 0.8505 (tp) REVERT: D 81 ASP cc_start: 0.8125 (p0) cc_final: 0.7602 (p0) REVERT: D 103 PHE cc_start: 0.8679 (m-80) cc_final: 0.8004 (m-80) REVERT: D 227 MET cc_start: 0.8561 (ttm) cc_final: 0.8114 (tpp) REVERT: D 287 TYR cc_start: 0.8842 (t80) cc_final: 0.8404 (t80) REVERT: D 425 PHE cc_start: 0.8667 (t80) cc_final: 0.8420 (t80) REVERT: D 429 LEU cc_start: 0.9087 (mt) cc_final: 0.8818 (mt) REVERT: E 151 MET cc_start: 0.8316 (ttp) cc_final: 0.8022 (ttp) REVERT: E 196 GLN cc_start: 0.9119 (tp40) cc_final: 0.8713 (tp40) REVERT: E 215 LYS cc_start: 0.8459 (mmmm) cc_final: 0.7995 (mmmm) REVERT: E 235 LEU cc_start: 0.9477 (mp) cc_final: 0.9068 (mp) REVERT: E 238 LEU cc_start: 0.8925 (mp) cc_final: 0.8647 (mp) REVERT: E 252 TYR cc_start: 0.9007 (t80) cc_final: 0.8426 (t80) REVERT: E 256 LEU cc_start: 0.9023 (mm) cc_final: 0.8565 (mm) REVERT: E 287 TYR cc_start: 0.8941 (t80) cc_final: 0.8633 (t80) REVERT: E 291 MET cc_start: 0.9176 (mmt) cc_final: 0.8689 (mmm) REVERT: E 296 LEU cc_start: 0.9316 (mt) cc_final: 0.9104 (mt) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.1824 time to fit residues: 119.7928 Evaluate side-chains 366 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 0.0370 chunk 133 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.083660 restraints weight = 36340.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086225 restraints weight = 24245.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088089 restraints weight = 18048.307| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12857 Z= 0.136 Angle : 0.718 11.916 17655 Z= 0.351 Chirality : 0.047 0.205 2167 Planarity : 0.003 0.032 2122 Dihedral : 5.491 59.564 1855 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1610 helix: 1.08 (0.22), residues: 525 sheet: -0.69 (0.26), residues: 430 loop : -1.21 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 65 HIS 0.006 0.001 HIS E 131 PHE 0.049 0.002 PHE D 289 TYR 0.020 0.001 TYR A 252 ARG 0.003 0.000 ARG C 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 4) link_NAG-ASN : angle 2.06888 ( 12) hydrogen bonds : bond 0.03874 ( 589) hydrogen bonds : angle 4.58599 ( 1665) SS BOND : bond 0.00174 ( 5) SS BOND : angle 2.06784 ( 10) covalent geometry : bond 0.00309 (12848) covalent geometry : angle 0.71449 (17633) *********************** 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 421 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9501 (tp) cc_final: 0.9260 (mm) REVERT: A 103 PHE cc_start: 0.8579 (m-80) cc_final: 0.8335 (m-80) REVERT: A 125 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8520 (ttpp) REVERT: A 227 MET cc_start: 0.8790 (tpp) cc_final: 0.8466 (tpp) REVERT: A 234 PHE cc_start: 0.8780 (t80) cc_final: 0.8546 (t80) REVERT: A 265 MET cc_start: 0.9304 (ttm) cc_final: 0.8630 (ttm) REVERT: A 287 TYR cc_start: 0.8532 (t80) cc_final: 0.7914 (t80) REVERT: A 296 LEU cc_start: 0.9177 (mt) cc_final: 0.8913 (mt) REVERT: A 425 PHE cc_start: 0.8629 (t80) cc_final: 0.8405 (t80) REVERT: B 265 MET cc_start: 0.8527 (ttt) cc_final: 0.7824 (ttm) REVERT: B 268 SER cc_start: 0.9173 (p) cc_final: 0.8922 (p) REVERT: B 269 ASP cc_start: 0.7817 (m-30) cc_final: 0.7612 (m-30) REVERT: B 287 TYR cc_start: 0.8507 (t80) cc_final: 0.8269 (t80) REVERT: C 65 TRP cc_start: 0.9432 (p90) cc_final: 0.9071 (p90) REVERT: C 151 MET cc_start: 0.8450 (ttp) cc_final: 0.7901 (ttp) REVERT: C 187 VAL cc_start: 0.9584 (t) cc_final: 0.9334 (t) REVERT: C 231 LEU cc_start: 0.9069 (mt) cc_final: 0.8818 (mt) REVERT: C 256 LEU cc_start: 0.8932 (mm) cc_final: 0.8624 (mm) REVERT: C 287 TYR cc_start: 0.8645 (t80) cc_final: 0.8291 (t80) REVERT: C 429 LEU cc_start: 0.9028 (mt) cc_final: 0.8733 (mt) REVERT: C 435 ILE cc_start: 0.8751 (pt) cc_final: 0.8468 (tp) REVERT: D 103 PHE cc_start: 0.8565 (m-80) cc_final: 0.7842 (m-80) REVERT: D 155 VAL cc_start: 0.9201 (p) cc_final: 0.8949 (p) REVERT: D 227 MET cc_start: 0.8593 (ttm) cc_final: 0.8165 (tpp) REVERT: D 266 MET cc_start: 0.8989 (ptt) cc_final: 0.8445 (ptp) REVERT: D 287 TYR cc_start: 0.8809 (t80) cc_final: 0.8389 (t80) REVERT: D 425 PHE cc_start: 0.8616 (t80) cc_final: 0.8291 (t80) REVERT: D 429 LEU cc_start: 0.9081 (mt) cc_final: 0.8748 (mt) REVERT: E 69 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7733 (mm-30) REVERT: E 127 MET cc_start: 0.7384 (ttt) cc_final: 0.5884 (mmt) REVERT: E 128 TRP cc_start: 0.8313 (t60) cc_final: 0.7678 (t60) REVERT: E 151 MET cc_start: 0.8493 (ttp) cc_final: 0.8203 (ttp) REVERT: E 196 GLN cc_start: 0.9078 (tp40) cc_final: 0.8704 (tp40) REVERT: E 215 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8033 (mmmm) REVERT: E 235 LEU cc_start: 0.9465 (mp) cc_final: 0.9036 (mt) REVERT: E 238 LEU cc_start: 0.8878 (mp) cc_final: 0.8616 (mp) REVERT: E 252 TYR cc_start: 0.8935 (t80) cc_final: 0.8437 (t80) REVERT: E 256 LEU cc_start: 0.8950 (mm) cc_final: 0.8736 (mm) REVERT: E 287 TYR cc_start: 0.8877 (t80) cc_final: 0.8594 (t80) REVERT: E 291 MET cc_start: 0.9140 (mmt) cc_final: 0.8605 (mmm) REVERT: E 296 LEU cc_start: 0.9281 (mt) cc_final: 0.9069 (mt) REVERT: E 301 MET cc_start: 0.7669 (mmm) cc_final: 0.7389 (mmm) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1925 time to fit residues: 127.9316 Evaluate side-chains 358 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 147 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.0030 chunk 52 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083556 restraints weight = 36095.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.086148 restraints weight = 24146.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.087988 restraints weight = 17981.880| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12857 Z= 0.130 Angle : 0.719 13.134 17655 Z= 0.351 Chirality : 0.046 0.202 2167 Planarity : 0.003 0.032 2122 Dihedral : 5.413 55.642 1855 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1610 helix: 1.09 (0.22), residues: 525 sheet: -0.66 (0.26), residues: 430 loop : -1.18 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 65 HIS 0.005 0.001 HIS E 131 PHE 0.028 0.002 PHE A 425 TYR 0.023 0.001 TYR D 252 ARG 0.003 0.000 ARG C 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 4) link_NAG-ASN : angle 1.98464 ( 12) hydrogen bonds : bond 0.03828 ( 589) hydrogen bonds : angle 4.55632 ( 1665) SS BOND : bond 0.00266 ( 5) SS BOND : angle 2.08980 ( 10) covalent geometry : bond 0.00296 (12848) covalent geometry : angle 0.71610 (17633) ********************** 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 411 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9494 (tp) cc_final: 0.9261 (mm) REVERT: A 103 PHE cc_start: 0.8593 (m-80) cc_final: 0.8319 (m-80) REVERT: A 125 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8532 (ttpp) REVERT: A 215 LYS cc_start: 0.8306 (mmmt) cc_final: 0.8097 (mmmt) REVERT: A 227 MET cc_start: 0.8774 (tpp) cc_final: 0.8479 (tpp) REVERT: A 234 PHE cc_start: 0.8764 (t80) cc_final: 0.8489 (t80) REVERT: A 265 MET cc_start: 0.9207 (ttm) cc_final: 0.9001 (ttm) REVERT: A 287 TYR cc_start: 0.8557 (t80) cc_final: 0.7695 (t80) REVERT: A 291 MET cc_start: 0.9138 (tpp) cc_final: 0.8352 (tpp) REVERT: A 296 LEU cc_start: 0.9217 (mt) cc_final: 0.9009 (mt) REVERT: A 425 PHE cc_start: 0.8650 (t80) cc_final: 0.8417 (t80) REVERT: B 85 LEU cc_start: 0.9064 (tp) cc_final: 0.8769 (pp) REVERT: B 227 MET cc_start: 0.8504 (ttm) cc_final: 0.7293 (tpp) REVERT: B 266 MET cc_start: 0.9073 (ptp) cc_final: 0.8802 (ptp) REVERT: B 269 ASP cc_start: 0.7929 (m-30) cc_final: 0.7702 (m-30) REVERT: B 287 TYR cc_start: 0.8599 (t80) cc_final: 0.8257 (t80) REVERT: C 65 TRP cc_start: 0.9433 (p90) cc_final: 0.9030 (p90) REVERT: C 151 MET cc_start: 0.8411 (ttp) cc_final: 0.7890 (ttp) REVERT: C 231 LEU cc_start: 0.9044 (mt) cc_final: 0.8811 (mt) REVERT: C 256 LEU cc_start: 0.8917 (mm) cc_final: 0.8713 (mm) REVERT: C 287 TYR cc_start: 0.8665 (t80) cc_final: 0.8254 (t80) REVERT: C 429 LEU cc_start: 0.9002 (mt) cc_final: 0.8710 (mt) REVERT: C 435 ILE cc_start: 0.8849 (pt) cc_final: 0.8557 (tt) REVERT: D 81 ASP cc_start: 0.7977 (p0) cc_final: 0.7725 (p0) REVERT: D 103 PHE cc_start: 0.8555 (m-80) cc_final: 0.7736 (m-80) REVERT: D 155 VAL cc_start: 0.9172 (p) cc_final: 0.8852 (p) REVERT: D 227 MET cc_start: 0.8453 (ttm) cc_final: 0.8118 (tpp) REVERT: D 263 LEU cc_start: 0.9380 (mt) cc_final: 0.9168 (mt) REVERT: D 266 MET cc_start: 0.9104 (ptt) cc_final: 0.8521 (ptp) REVERT: D 287 TYR cc_start: 0.8711 (t80) cc_final: 0.8310 (t80) REVERT: D 425 PHE cc_start: 0.8615 (t80) cc_final: 0.8299 (t80) REVERT: D 429 LEU cc_start: 0.9070 (mt) cc_final: 0.8749 (mt) REVERT: E 125 LYS cc_start: 0.6649 (tptp) cc_final: 0.6272 (tptp) REVERT: E 151 MET cc_start: 0.8357 (ttp) cc_final: 0.8068 (ttp) REVERT: E 196 GLN cc_start: 0.9110 (tp40) cc_final: 0.8715 (tp40) REVERT: E 215 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8024 (mmmm) REVERT: E 235 LEU cc_start: 0.9460 (mp) cc_final: 0.9075 (mp) REVERT: E 238 LEU cc_start: 0.8875 (mp) cc_final: 0.8608 (mp) REVERT: E 252 TYR cc_start: 0.8934 (t80) cc_final: 0.8433 (t80) REVERT: E 287 TYR cc_start: 0.8914 (t80) cc_final: 0.8631 (t80) REVERT: E 291 MET cc_start: 0.9141 (mmt) cc_final: 0.8648 (mmm) REVERT: E 296 LEU cc_start: 0.9290 (mt) cc_final: 0.9059 (mt) REVERT: E 301 MET cc_start: 0.7706 (mmm) cc_final: 0.7429 (mmm) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.3240 time to fit residues: 218.1071 Evaluate side-chains 374 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083522 restraints weight = 36463.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086020 restraints weight = 24382.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.087918 restraints weight = 18287.967| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12857 Z= 0.131 Angle : 0.731 14.797 17655 Z= 0.355 Chirality : 0.046 0.206 2167 Planarity : 0.003 0.032 2122 Dihedral : 5.395 55.227 1855 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1610 helix: 1.02 (0.22), residues: 525 sheet: -0.68 (0.26), residues: 440 loop : -1.24 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 65 HIS 0.005 0.001 HIS E 131 PHE 0.028 0.002 PHE A 425 TYR 0.039 0.001 TYR E 67 ARG 0.006 0.000 ARG E 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 4) link_NAG-ASN : angle 1.95056 ( 12) hydrogen bonds : bond 0.03792 ( 589) hydrogen bonds : angle 4.57376 ( 1665) SS BOND : bond 0.00320 ( 5) SS BOND : angle 2.11859 ( 10) covalent geometry : bond 0.00299 (12848) covalent geometry : angle 0.72764 (17633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.23 seconds wall clock time: 81 minutes 54.99 seconds (4914.99 seconds total)