Starting phenix.real_space_refine on Mon Dec 30 08:20:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bx5_16308/12_2024/8bx5_16308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bx5_16308/12_2024/8bx5_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_16308/12_2024/8bx5_16308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bx5_16308/12_2024/8bx5_16308.map" model { file = "/net/cci-nas-00/data/ceres_data/8bx5_16308/12_2024/8bx5_16308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bx5_16308/12_2024/8bx5_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.82, per 1000 atoms: 0.62 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: 2.99 Conformation dependent library (CDL) restraints added in 1.7 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: 1.25 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: 3.42 Time building geometry restraints manager: 3.51 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: 0.420 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.460 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- 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 12848 Z= 0.231 Angle : 0.784 9.027 17633 Z= 0.409 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 *********************** 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 : 1.402 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: 0.1968 time to fit residues: 139.4275 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 : 1.388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 12848 Z= 0.283 Angle : 0.693 12.138 17633 Z= 0.345 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 *********************** 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 : 1.463 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 72 ASP cc_start: 0.8245 (t70) cc_final: 0.8024 (t0) REVERT: A 125 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8056 (tttm) REVERT: A 173 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8194 (tp-100) REVERT: A 234 PHE cc_start: 0.8882 (t80) cc_final: 0.8456 (t80) REVERT: A 287 TYR cc_start: 0.9053 (t80) cc_final: 0.8512 (t80) REVERT: A 296 LEU cc_start: 0.9152 (mt) cc_final: 0.8853 (mt) REVERT: B 102 LEU cc_start: 0.8404 (tp) cc_final: 0.8158 (tp) REVERT: B 103 PHE cc_start: 0.8952 (m-10) cc_final: 0.8636 (m-80) REVERT: B 256 LEU cc_start: 0.9557 (mm) cc_final: 0.9302 (mm) REVERT: B 266 MET cc_start: 0.9201 (ppp) cc_final: 0.8846 (ppp) REVERT: B 269 ASP cc_start: 0.7853 (m-30) cc_final: 0.7511 (m-30) REVERT: B 287 TYR cc_start: 0.8819 (t80) cc_final: 0.8419 (t80) REVERT: B 301 MET cc_start: 0.9014 (mmp) cc_final: 0.8432 (ptm) REVERT: C 231 LEU cc_start: 0.8956 (mt) cc_final: 0.8628 (mt) REVERT: C 238 LEU cc_start: 0.9035 (mp) cc_final: 0.8810 (mp) REVERT: C 252 TYR cc_start: 0.9178 (t80) cc_final: 0.8934 (t80) REVERT: C 256 LEU cc_start: 0.9464 (mm) cc_final: 0.9245 (mm) REVERT: C 266 MET cc_start: 0.9226 (ptp) cc_final: 0.8928 (ptm) REVERT: C 269 ASP cc_start: 0.8439 (m-30) cc_final: 0.8140 (m-30) REVERT: C 287 TYR cc_start: 0.9035 (t80) cc_final: 0.8396 (t80) REVERT: C 301 MET cc_start: 0.9026 (mmp) cc_final: 0.8551 (ppp) REVERT: C 435 ILE cc_start: 0.8989 (pt) cc_final: 0.8707 (tp) REVERT: D 103 PHE cc_start: 0.8364 (m-80) cc_final: 0.7770 (m-80) REVERT: D 140 LEU cc_start: 0.8483 (mt) cc_final: 0.8264 (mt) REVERT: D 184 GLU cc_start: 0.8869 (pm20) cc_final: 0.8605 (pm20) REVERT: D 252 TYR cc_start: 0.9208 (t80) cc_final: 0.8606 (t80) REVERT: D 256 LEU cc_start: 0.9536 (mm) cc_final: 0.9330 (mm) REVERT: D 266 MET cc_start: 0.9249 (ptp) cc_final: 0.9027 (ptp) REVERT: D 287 TYR cc_start: 0.9270 (t80) cc_final: 0.8648 (t80) REVERT: D 425 PHE cc_start: 0.8478 (t80) cc_final: 0.8177 (t80) REVERT: E 62 THR cc_start: 0.8924 (p) cc_final: 0.8656 (p) REVERT: E 74 GLN cc_start: 0.8465 (mp10) cc_final: 0.8194 (mp10) REVERT: E 215 LYS cc_start: 0.8343 (mmmm) cc_final: 0.7942 (mmmm) REVERT: E 225 PHE cc_start: 0.8555 (m-80) cc_final: 0.8075 (m-80) REVERT: E 227 MET cc_start: 0.8506 (ttm) cc_final: 0.8290 (ttm) REVERT: E 234 PHE cc_start: 0.8608 (t80) cc_final: 0.8296 (t80) REVERT: E 235 LEU cc_start: 0.9364 (mt) cc_final: 0.9103 (mt) REVERT: E 238 LEU cc_start: 0.8940 (mp) cc_final: 0.8567 (mp) REVERT: E 252 TYR cc_start: 0.8899 (t80) cc_final: 0.8603 (t80) REVERT: E 287 TYR cc_start: 0.8951 (t80) cc_final: 0.8628 (t80) REVERT: E 296 LEU cc_start: 0.9358 (mt) cc_final: 0.9153 (mt) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.1942 time to fit residues: 124.1683 Evaluate side-chains 377 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 120 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 40 optimal weight: 0.0030 chunk 145 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12848 Z= 0.181 Angle : 0.662 10.840 17633 Z= 0.325 Chirality : 0.045 0.257 2167 Planarity : 0.003 0.031 2122 Dihedral : 5.960 56.505 1855 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % 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: -0.62 (0.21), residues: 1610 helix: 1.25 (0.22), residues: 525 sheet: -0.98 (0.26), residues: 420 loop : -1.31 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 185 HIS 0.006 0.001 HIS A 68 PHE 0.033 0.002 PHE D 289 TYR 0.017 0.001 TYR B 223 ARG 0.009 0.000 ARG B 216 *********************** 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 439 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 438 time to evaluate : 1.431 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: 0.9376 (tp) cc_final: 0.9166 (mm) REVERT: A 72 ASP cc_start: 0.8441 (t70) cc_final: 0.7800 (t0) REVERT: A 173 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8069 (tp-100) REVERT: A 234 PHE cc_start: 0.8748 (t80) cc_final: 0.8358 (t80) REVERT: A 241 PHE cc_start: 0.8573 (m-80) cc_final: 0.8168 (m-10) REVERT: A 256 LEU cc_start: 0.9593 (mm) cc_final: 0.9370 (mm) REVERT: A 269 ASP cc_start: 0.7912 (m-30) cc_final: 0.7697 (m-30) REVERT: A 287 TYR cc_start: 0.8905 (t80) cc_final: 0.8156 (t80) REVERT: A 296 LEU cc_start: 0.9037 (mt) cc_final: 0.8693 (mt) REVERT: B 72 ASP cc_start: 0.8474 (t70) cc_final: 0.8095 (t0) REVERT: B 78 ASN cc_start: 0.8293 (p0) cc_final: 0.7932 (p0) REVERT: B 85 LEU cc_start: 0.9122 (tp) cc_final: 0.8846 (pp) REVERT: B 103 PHE cc_start: 0.9058 (m-10) cc_final: 0.8778 (m-80) REVERT: B 256 LEU cc_start: 0.9426 (mm) cc_final: 0.9176 (mm) REVERT: B 265 MET cc_start: 0.6945 (ttp) cc_final: 0.6568 (tmm) REVERT: B 266 MET cc_start: 0.9103 (ppp) cc_final: 0.8617 (ppp) REVERT: B 269 ASP cc_start: 0.7753 (m-30) cc_final: 0.7347 (m-30) REVERT: B 287 TYR cc_start: 0.8817 (t80) cc_final: 0.8353 (t80) REVERT: B 291 MET cc_start: 0.9328 (tpp) cc_final: 0.8830 (mmm) REVERT: B 301 MET cc_start: 0.8943 (mmp) cc_final: 0.8425 (ptm) REVERT: C 231 LEU cc_start: 0.9025 (mt) cc_final: 0.8772 (mt) REVERT: C 238 LEU cc_start: 0.9029 (mp) cc_final: 0.8775 (mp) REVERT: C 252 TYR cc_start: 0.9130 (t80) cc_final: 0.8849 (t80) REVERT: C 256 LEU cc_start: 0.9398 (mm) cc_final: 0.9166 (mm) REVERT: C 266 MET cc_start: 0.9202 (ptp) cc_final: 0.8848 (ptm) REVERT: C 269 ASP cc_start: 0.8401 (m-30) cc_final: 0.8129 (m-30) REVERT: C 287 TYR cc_start: 0.8985 (t80) cc_final: 0.8440 (t80) REVERT: C 301 MET cc_start: 0.8960 (mmp) cc_final: 0.8549 (ppp) REVERT: C 435 ILE cc_start: 0.8932 (pt) cc_final: 0.8636 (tp) REVERT: D 102 LEU cc_start: 0.9279 (tt) cc_final: 0.8927 (tp) REVERT: D 103 PHE cc_start: 0.8418 (m-80) cc_final: 0.7750 (m-80) REVERT: D 252 TYR cc_start: 0.9160 (t80) cc_final: 0.8600 (t80) REVERT: D 256 LEU cc_start: 0.9455 (mm) cc_final: 0.9236 (mm) REVERT: D 266 MET cc_start: 0.9212 (ptp) cc_final: 0.8839 (ptt) REVERT: D 287 TYR cc_start: 0.9261 (t80) cc_final: 0.8651 (t80) REVERT: D 289 PHE cc_start: 0.9397 (t80) cc_final: 0.9038 (t80) REVERT: D 425 PHE cc_start: 0.8346 (t80) cc_final: 0.8025 (t80) REVERT: E 62 THR cc_start: 0.8995 (p) cc_final: 0.8634 (t) REVERT: E 74 GLN cc_start: 0.8489 (mp10) cc_final: 0.8232 (mp10) REVERT: E 129 VAL cc_start: 0.9558 (t) cc_final: 0.9352 (t) REVERT: E 151 MET cc_start: 0.7892 (ttp) cc_final: 0.7652 (ttp) REVERT: E 196 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8726 (tp40) REVERT: E 215 LYS cc_start: 0.8511 (mmmm) cc_final: 0.8293 (mmmm) REVERT: E 225 PHE cc_start: 0.8498 (m-80) cc_final: 0.7955 (m-80) REVERT: E 232 LEU cc_start: 0.9436 (mp) cc_final: 0.9226 (mp) REVERT: E 234 PHE cc_start: 0.8544 (t80) cc_final: 0.8296 (t80) REVERT: E 235 LEU cc_start: 0.9391 (mt) cc_final: 0.9167 (mt) REVERT: E 238 LEU cc_start: 0.8852 (mp) cc_final: 0.8556 (mp) REVERT: E 239 MET cc_start: 0.8781 (ptm) cc_final: 0.8480 (ppp) REVERT: E 252 TYR cc_start: 0.9051 (t80) cc_final: 0.8751 (t80) REVERT: E 256 LEU cc_start: 0.9401 (mm) cc_final: 0.9167 (mm) REVERT: E 287 TYR cc_start: 0.8982 (t80) cc_final: 0.8759 (t80) REVERT: E 296 LEU cc_start: 0.9316 (mt) cc_final: 0.9082 (mt) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.1950 time to fit residues: 134.1458 Evaluate side-chains 377 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12848 Z= 0.325 Angle : 0.680 9.038 17633 Z= 0.349 Chirality : 0.046 0.263 2167 Planarity : 0.004 0.035 2122 Dihedral : 5.646 54.144 1855 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.90 % Rotamer: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.21), residues: 1610 helix: 1.25 (0.22), residues: 525 sheet: -0.83 (0.26), residues: 400 loop : -1.26 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 65 HIS 0.017 0.001 HIS E 131 PHE 0.024 0.002 PHE B 428 TYR 0.022 0.002 TYR B 284 ARG 0.003 0.000 ARG B 216 *********************** 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 423 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 422 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9456 (tp) cc_final: 0.9246 (mm) REVERT: A 72 ASP cc_start: 0.8493 (t70) cc_final: 0.7814 (t0) REVERT: A 125 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8260 (tttt) REVERT: A 127 MET cc_start: 0.7176 (ttt) cc_final: 0.6975 (ttt) REVERT: A 140 LEU cc_start: 0.8993 (mp) cc_final: 0.8648 (mt) REVERT: A 173 GLN cc_start: 0.8535 (tp-100) cc_final: 0.8139 (tp-100) REVERT: A 256 LEU cc_start: 0.9633 (mm) cc_final: 0.9420 (mm) REVERT: A 265 MET cc_start: 0.9035 (ttm) cc_final: 0.8525 (ttm) REVERT: A 287 TYR cc_start: 0.9116 (t80) cc_final: 0.8273 (t80) REVERT: A 296 LEU cc_start: 0.9181 (mt) cc_final: 0.8844 (mt) REVERT: B 72 ASP cc_start: 0.8554 (t70) cc_final: 0.8089 (t0) REVERT: B 102 LEU cc_start: 0.8660 (tp) cc_final: 0.8391 (tp) REVERT: B 103 PHE cc_start: 0.9112 (m-10) cc_final: 0.8683 (m-80) REVERT: B 269 ASP cc_start: 0.7864 (m-30) cc_final: 0.7593 (m-30) REVERT: B 287 TYR cc_start: 0.8886 (t80) cc_final: 0.8478 (t80) REVERT: B 301 MET cc_start: 0.9100 (mmp) cc_final: 0.8445 (ptm) REVERT: B 428 PHE cc_start: 0.9208 (m-80) cc_final: 0.8995 (m-80) REVERT: C 58 HIS cc_start: 0.8629 (m-70) cc_final: 0.8414 (m-70) REVERT: C 65 TRP cc_start: 0.9105 (p90) cc_final: 0.8815 (p90) REVERT: C 187 VAL cc_start: 0.9525 (t) cc_final: 0.9046 (t) REVERT: C 238 LEU cc_start: 0.9161 (mp) cc_final: 0.8907 (mp) REVERT: C 252 TYR cc_start: 0.9140 (t80) cc_final: 0.8900 (t80) REVERT: C 256 LEU cc_start: 0.9455 (mm) cc_final: 0.9194 (mm) REVERT: C 269 ASP cc_start: 0.8524 (m-30) cc_final: 0.8280 (m-30) REVERT: C 275 LEU cc_start: 0.8751 (tp) cc_final: 0.8423 (tp) REVERT: C 287 TYR cc_start: 0.9127 (t80) cc_final: 0.8504 (t80) REVERT: C 301 MET cc_start: 0.9003 (mmp) cc_final: 0.8547 (ppp) REVERT: C 435 ILE cc_start: 0.9041 (pt) cc_final: 0.8758 (tp) REVERT: D 103 PHE cc_start: 0.8523 (m-80) cc_final: 0.7880 (m-80) REVERT: D 184 GLU cc_start: 0.8832 (pm20) cc_final: 0.8625 (pm20) REVERT: D 252 TYR cc_start: 0.9272 (t80) cc_final: 0.8764 (t80) REVERT: D 256 LEU cc_start: 0.9448 (mm) cc_final: 0.9236 (mm) REVERT: D 287 TYR cc_start: 0.9325 (t80) cc_final: 0.8721 (t80) REVERT: D 289 PHE cc_start: 0.9595 (t80) cc_final: 0.9013 (t80) REVERT: D 295 ASN cc_start: 0.9192 (p0) cc_final: 0.8897 (p0) REVERT: D 425 PHE cc_start: 0.8628 (t80) cc_final: 0.8375 (t80) REVERT: E 74 GLN cc_start: 0.8568 (mp10) cc_final: 0.8302 (mp10) REVERT: E 151 MET cc_start: 0.7757 (ttp) cc_final: 0.7550 (ttp) REVERT: E 196 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8635 (tp40) REVERT: E 215 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8256 (mmmm) REVERT: E 225 PHE cc_start: 0.8432 (m-80) cc_final: 0.7941 (m-80) REVERT: E 227 MET cc_start: 0.8530 (ttm) cc_final: 0.8281 (ttm) REVERT: E 234 PHE cc_start: 0.8764 (t80) cc_final: 0.8363 (t80) REVERT: E 238 LEU cc_start: 0.9010 (mp) cc_final: 0.8686 (mp) REVERT: E 256 LEU cc_start: 0.9494 (mm) cc_final: 0.9247 (mm) REVERT: E 296 LEU cc_start: 0.9434 (mt) cc_final: 0.9206 (mt) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.1881 time to fit residues: 124.0375 Evaluate side-chains 349 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** E 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12848 Z= 0.325 Angle : 0.700 9.963 17633 Z= 0.356 Chirality : 0.046 0.221 2167 Planarity : 0.004 0.033 2122 Dihedral : 5.656 53.502 1855 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.04 % Favored : 95.84 % Rotamer: Outliers : 0.08 % Allowed : 5.32 % Favored : 94.60 % 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: -0.57 (0.21), residues: 1610 helix: 1.24 (0.22), residues: 525 sheet: -0.86 (0.26), residues: 400 loop : -1.31 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 65 HIS 0.006 0.001 HIS C 161 PHE 0.031 0.002 PHE A 425 TYR 0.019 0.002 TYR E 287 ARG 0.004 0.001 ARG B 216 *********************** 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 418 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.8892 (m-70) cc_final: 0.8598 (m-70) REVERT: A 72 ASP cc_start: 0.8414 (t70) cc_final: 0.7551 (t0) REVERT: A 125 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8300 (tttt) REVERT: A 140 LEU cc_start: 0.9166 (mp) cc_final: 0.8743 (mt) REVERT: A 215 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8354 (mmmt) REVERT: A 234 PHE cc_start: 0.9050 (t80) cc_final: 0.8815 (t80) REVERT: A 256 LEU cc_start: 0.9602 (mm) cc_final: 0.9378 (mm) REVERT: A 287 TYR cc_start: 0.9114 (t80) cc_final: 0.8121 (t80) REVERT: A 289 PHE cc_start: 0.9685 (t80) cc_final: 0.9481 (t80) REVERT: A 296 LEU cc_start: 0.9216 (mt) cc_final: 0.8847 (mt) REVERT: B 227 MET cc_start: 0.8548 (ttm) cc_final: 0.8159 (tpp) REVERT: B 231 LEU cc_start: 0.9136 (pp) cc_final: 0.8391 (mt) REVERT: B 256 LEU cc_start: 0.9502 (mm) cc_final: 0.9260 (mm) REVERT: B 266 MET cc_start: 0.9095 (ppp) cc_final: 0.8851 (ppp) REVERT: B 269 ASP cc_start: 0.7942 (m-30) cc_final: 0.7655 (m-30) REVERT: B 287 TYR cc_start: 0.8939 (t80) cc_final: 0.8499 (t80) REVERT: B 301 MET cc_start: 0.9111 (mmp) cc_final: 0.8455 (ptm) REVERT: C 58 HIS cc_start: 0.8797 (m-70) cc_final: 0.8410 (m-70) REVERT: C 65 TRP cc_start: 0.9080 (p90) cc_final: 0.8832 (p90) REVERT: C 252 TYR cc_start: 0.9212 (t80) cc_final: 0.8929 (t80) REVERT: C 256 LEU cc_start: 0.9469 (mm) cc_final: 0.9247 (mm) REVERT: C 275 LEU cc_start: 0.8959 (tp) cc_final: 0.8713 (tp) REVERT: C 287 TYR cc_start: 0.9238 (t80) cc_final: 0.8562 (t80) REVERT: C 301 MET cc_start: 0.9002 (mmp) cc_final: 0.8680 (ppp) REVERT: C 435 ILE cc_start: 0.9183 (pt) cc_final: 0.8896 (tp) REVERT: D 58 HIS cc_start: 0.8965 (m-70) cc_final: 0.8740 (m-70) REVERT: D 62 THR cc_start: 0.8796 (p) cc_final: 0.8548 (p) REVERT: D 82 TYR cc_start: 0.7813 (m-80) cc_final: 0.7578 (m-10) REVERT: D 103 PHE cc_start: 0.8656 (m-80) cc_final: 0.8129 (m-80) REVERT: D 155 VAL cc_start: 0.8941 (p) cc_final: 0.8630 (p) REVERT: D 184 GLU cc_start: 0.8818 (pm20) cc_final: 0.8614 (pm20) REVERT: D 252 TYR cc_start: 0.9282 (t80) cc_final: 0.8808 (t80) REVERT: D 266 MET cc_start: 0.9007 (ptm) cc_final: 0.8765 (ptp) REVERT: D 287 TYR cc_start: 0.9315 (t80) cc_final: 0.8710 (t80) REVERT: D 295 ASN cc_start: 0.9158 (p0) cc_final: 0.8823 (p0) REVERT: D 425 PHE cc_start: 0.8665 (t80) cc_final: 0.8403 (t80) REVERT: E 62 THR cc_start: 0.8958 (p) cc_final: 0.8603 (t) REVERT: E 184 GLU cc_start: 0.8813 (pm20) cc_final: 0.8590 (pm20) REVERT: E 196 GLN cc_start: 0.9110 (tp40) cc_final: 0.8626 (tp40) REVERT: E 215 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8232 (mmmm) REVERT: E 225 PHE cc_start: 0.8458 (m-80) cc_final: 0.7941 (m-80) REVERT: E 227 MET cc_start: 0.8574 (ttm) cc_final: 0.8361 (ttm) REVERT: E 234 PHE cc_start: 0.9032 (t80) cc_final: 0.8743 (t80) REVERT: E 238 LEU cc_start: 0.9030 (mp) cc_final: 0.8601 (mp) REVERT: E 252 TYR cc_start: 0.9283 (t80) cc_final: 0.9055 (t80) REVERT: E 256 LEU cc_start: 0.9469 (mm) cc_final: 0.9267 (mm) REVERT: E 287 TYR cc_start: 0.9135 (t80) cc_final: 0.8283 (t80) REVERT: E 296 LEU cc_start: 0.9405 (mt) cc_final: 0.9171 (mt) outliers start: 1 outliers final: 0 residues processed: 417 average time/residue: 0.1866 time to fit residues: 121.9161 Evaluate side-chains 353 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12848 Z= 0.219 Angle : 0.673 10.810 17633 Z= 0.335 Chirality : 0.046 0.187 2167 Planarity : 0.003 0.030 2122 Dihedral : 5.597 53.990 1855 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 1.36 (0.22), residues: 525 sheet: -0.94 (0.26), residues: 410 loop : -1.28 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 159 HIS 0.006 0.001 HIS D 161 PHE 0.025 0.002 PHE A 289 TYR 0.018 0.002 TYR A 252 ARG 0.003 0.000 ARG B 249 *********************** 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 432 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.8949 (m-70) cc_final: 0.8726 (m-70) REVERT: A 72 ASP cc_start: 0.8531 (t70) cc_final: 0.7601 (t0) REVERT: A 125 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8507 (tttm) REVERT: A 127 MET cc_start: 0.7356 (ttt) cc_final: 0.6952 (ttt) REVERT: A 140 LEU cc_start: 0.9271 (mp) cc_final: 0.8924 (mt) REVERT: A 265 MET cc_start: 0.8707 (ttm) cc_final: 0.8174 (ttm) REVERT: A 287 TYR cc_start: 0.9037 (t80) cc_final: 0.7876 (t80) REVERT: A 296 LEU cc_start: 0.9184 (mt) cc_final: 0.8786 (mt) REVERT: A 425 PHE cc_start: 0.8685 (t80) cc_final: 0.8470 (t80) REVERT: B 72 ASP cc_start: 0.8492 (t70) cc_final: 0.8053 (t0) REVERT: B 103 PHE cc_start: 0.9153 (m-10) cc_final: 0.8760 (m-80) REVERT: B 252 TYR cc_start: 0.9220 (t80) cc_final: 0.8881 (t80) REVERT: B 256 LEU cc_start: 0.9526 (mm) cc_final: 0.9277 (mm) REVERT: B 266 MET cc_start: 0.9036 (ppp) cc_final: 0.8673 (ppp) REVERT: B 287 TYR cc_start: 0.8882 (t80) cc_final: 0.8413 (t80) REVERT: B 291 MET cc_start: 0.9211 (tpp) cc_final: 0.8981 (mmt) REVERT: B 301 MET cc_start: 0.9093 (mmp) cc_final: 0.8460 (ptm) REVERT: B 428 PHE cc_start: 0.9338 (m-80) cc_final: 0.9074 (m-80) REVERT: C 58 HIS cc_start: 0.8801 (m-70) cc_final: 0.8418 (m-70) REVERT: C 65 TRP cc_start: 0.9091 (p90) cc_final: 0.8832 (p90) REVERT: C 231 LEU cc_start: 0.8978 (mt) cc_final: 0.8633 (mt) REVERT: C 252 TYR cc_start: 0.9179 (t80) cc_final: 0.8905 (t80) REVERT: C 256 LEU cc_start: 0.9426 (mm) cc_final: 0.9197 (mm) REVERT: C 287 TYR cc_start: 0.9139 (t80) cc_final: 0.8481 (t80) REVERT: C 301 MET cc_start: 0.8998 (mmp) cc_final: 0.8723 (ppp) REVERT: C 435 ILE cc_start: 0.9103 (pt) cc_final: 0.8850 (tp) REVERT: D 58 HIS cc_start: 0.8958 (m-70) cc_final: 0.8709 (m-70) REVERT: D 82 TYR cc_start: 0.7804 (m-80) cc_final: 0.7572 (m-10) REVERT: D 103 PHE cc_start: 0.8689 (m-80) cc_final: 0.8157 (m-80) REVERT: D 227 MET cc_start: 0.8215 (ttm) cc_final: 0.7985 (tpp) REVERT: D 287 TYR cc_start: 0.9290 (t80) cc_final: 0.8664 (t80) REVERT: D 295 ASN cc_start: 0.9123 (p0) cc_final: 0.8779 (p0) REVERT: D 301 MET cc_start: 0.8677 (tpt) cc_final: 0.8235 (mmm) REVERT: D 425 PHE cc_start: 0.8609 (t80) cc_final: 0.8353 (t80) REVERT: E 62 THR cc_start: 0.8957 (p) cc_final: 0.8600 (t) REVERT: E 69 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 196 GLN cc_start: 0.9151 (tp40) cc_final: 0.8682 (tp40) REVERT: E 215 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8098 (mmmm) REVERT: E 227 MET cc_start: 0.8550 (ttm) cc_final: 0.8339 (ttm) REVERT: E 238 LEU cc_start: 0.8954 (mp) cc_final: 0.8615 (mp) REVERT: E 252 TYR cc_start: 0.9234 (t80) cc_final: 0.8978 (t80) REVERT: E 266 MET cc_start: 0.8949 (ppp) cc_final: 0.8128 (ppp) REVERT: E 287 TYR cc_start: 0.8931 (t80) cc_final: 0.8644 (t80) REVERT: E 296 LEU cc_start: 0.9412 (mt) cc_final: 0.9166 (mt) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1913 time to fit residues: 129.1879 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 : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.0170 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12848 Z= 0.225 Angle : 0.678 14.150 17633 Z= 0.337 Chirality : 0.046 0.232 2167 Planarity : 0.003 0.031 2122 Dihedral : 5.651 54.300 1855 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -0.51 (0.21), residues: 1610 helix: 1.36 (0.22), residues: 525 sheet: -0.89 (0.26), residues: 410 loop : -1.30 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 65 HIS 0.005 0.001 HIS D 161 PHE 0.026 0.002 PHE E 234 TYR 0.021 0.001 TYR D 252 ARG 0.014 0.001 ARG C 216 *********************** 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 426 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.442 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 58 HIS cc_start: 0.9031 (m-70) cc_final: 0.8721 (m-70) REVERT: A 72 ASP cc_start: 0.8311 (t70) cc_final: 0.7672 (t0) REVERT: A 140 LEU cc_start: 0.9227 (mp) cc_final: 0.8840 (mt) REVERT: A 173 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8416 (tp-100) REVERT: A 234 PHE cc_start: 0.9106 (t80) cc_final: 0.8549 (t80) REVERT: A 256 LEU cc_start: 0.9583 (mm) cc_final: 0.9381 (mm) REVERT: A 265 MET cc_start: 0.8403 (ttm) cc_final: 0.8155 (ttm) REVERT: A 287 TYR cc_start: 0.9058 (t80) cc_final: 0.7999 (t80) REVERT: A 291 MET cc_start: 0.9255 (ttm) cc_final: 0.8787 (ttm) REVERT: B 69 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 72 ASP cc_start: 0.8501 (t70) cc_final: 0.8051 (t0) REVERT: B 252 TYR cc_start: 0.9190 (t80) cc_final: 0.8827 (t80) REVERT: B 256 LEU cc_start: 0.9491 (mm) cc_final: 0.9030 (mm) REVERT: B 266 MET cc_start: 0.9038 (ppp) cc_final: 0.8676 (ppp) REVERT: B 269 ASP cc_start: 0.7919 (m-30) cc_final: 0.7665 (m-30) REVERT: B 287 TYR cc_start: 0.8876 (t80) cc_final: 0.8372 (t80) REVERT: B 296 LEU cc_start: 0.9111 (mt) cc_final: 0.8887 (mt) REVERT: B 301 MET cc_start: 0.9096 (mmp) cc_final: 0.8455 (ptm) REVERT: C 58 HIS cc_start: 0.8828 (m-70) cc_final: 0.8436 (m-70) REVERT: C 65 TRP cc_start: 0.9121 (p90) cc_final: 0.8865 (p90) REVERT: C 133 ARG cc_start: 0.7460 (ttp-110) cc_final: 0.6801 (ttp-110) REVERT: C 231 LEU cc_start: 0.8975 (mt) cc_final: 0.8655 (mt) REVERT: C 252 TYR cc_start: 0.9194 (t80) cc_final: 0.8836 (t80) REVERT: C 256 LEU cc_start: 0.9456 (mm) cc_final: 0.9208 (mm) REVERT: C 287 TYR cc_start: 0.9139 (t80) cc_final: 0.8559 (t80) REVERT: C 301 MET cc_start: 0.8993 (mmp) cc_final: 0.8742 (ppp) REVERT: C 435 ILE cc_start: 0.9112 (pt) cc_final: 0.8854 (tp) REVERT: D 58 HIS cc_start: 0.8995 (m-70) cc_final: 0.8769 (m-70) REVERT: D 82 TYR cc_start: 0.7822 (m-80) cc_final: 0.7579 (m-10) REVERT: D 103 PHE cc_start: 0.8751 (m-80) cc_final: 0.8219 (m-80) REVERT: D 155 VAL cc_start: 0.8866 (p) cc_final: 0.8619 (p) REVERT: D 184 GLU cc_start: 0.8782 (pm20) cc_final: 0.8568 (pm20) REVERT: D 287 TYR cc_start: 0.9305 (t80) cc_final: 0.8651 (t80) REVERT: D 295 ASN cc_start: 0.9139 (p0) cc_final: 0.8772 (p0) REVERT: D 301 MET cc_start: 0.8685 (tpt) cc_final: 0.8273 (mmm) REVERT: D 425 PHE cc_start: 0.8622 (t80) cc_final: 0.8360 (t80) REVERT: E 74 GLN cc_start: 0.8546 (mp10) cc_final: 0.8306 (mp10) REVERT: E 184 GLU cc_start: 0.8781 (pm20) cc_final: 0.8569 (pm20) REVERT: E 196 GLN cc_start: 0.9122 (tp40) cc_final: 0.8658 (tp40) REVERT: E 215 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8078 (mmmm) REVERT: E 235 LEU cc_start: 0.9462 (mt) cc_final: 0.9221 (mm) REVERT: E 238 LEU cc_start: 0.8943 (mp) cc_final: 0.8665 (mp) REVERT: E 252 TYR cc_start: 0.9268 (t80) cc_final: 0.9066 (t80) REVERT: E 266 MET cc_start: 0.8992 (ppp) cc_final: 0.8210 (ppp) REVERT: E 287 TYR cc_start: 0.9016 (t80) cc_final: 0.8394 (t80) REVERT: E 291 MET cc_start: 0.9203 (tpp) cc_final: 0.8838 (tpp) REVERT: E 296 LEU cc_start: 0.9415 (mt) cc_final: 0.9187 (mt) REVERT: E 301 MET cc_start: 0.8270 (mmm) cc_final: 0.8068 (mmm) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.1973 time to fit residues: 129.2504 Evaluate side-chains 369 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12848 Z= 0.230 Angle : 0.703 12.842 17633 Z= 0.348 Chirality : 0.047 0.215 2167 Planarity : 0.004 0.033 2122 Dihedral : 5.774 59.288 1855 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -0.48 (0.21), residues: 1610 helix: 1.35 (0.22), residues: 525 sheet: -0.82 (0.27), residues: 410 loop : -1.30 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 159 HIS 0.005 0.001 HIS B 161 PHE 0.040 0.002 PHE D 289 TYR 0.027 0.001 TYR D 252 ARG 0.009 0.001 ARG C 216 *********************** 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 424 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.410 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 58 HIS cc_start: 0.9076 (m-70) cc_final: 0.8706 (m-70) REVERT: A 72 ASP cc_start: 0.8457 (t70) cc_final: 0.7845 (t0) REVERT: A 125 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8524 (ttpp) REVERT: A 140 LEU cc_start: 0.9155 (mp) cc_final: 0.8825 (mt) REVERT: A 173 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8407 (tp-100) REVERT: A 234 PHE cc_start: 0.9109 (t80) cc_final: 0.8576 (t80) REVERT: A 287 TYR cc_start: 0.9063 (t80) cc_final: 0.8342 (t80) REVERT: B 69 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 72 ASP cc_start: 0.8505 (t70) cc_final: 0.8218 (t0) REVERT: B 227 MET cc_start: 0.8234 (tpp) cc_final: 0.8029 (tpp) REVERT: B 252 TYR cc_start: 0.9193 (t80) cc_final: 0.8986 (t80) REVERT: B 256 LEU cc_start: 0.9496 (mm) cc_final: 0.9152 (mm) REVERT: B 266 MET cc_start: 0.9048 (ppp) cc_final: 0.8677 (ppp) REVERT: B 287 TYR cc_start: 0.8921 (t80) cc_final: 0.8502 (t80) REVERT: B 296 LEU cc_start: 0.9185 (mt) cc_final: 0.8935 (mt) REVERT: B 301 MET cc_start: 0.9100 (mmp) cc_final: 0.8457 (ptm) REVERT: C 58 HIS cc_start: 0.8850 (m-70) cc_final: 0.8444 (m-70) REVERT: C 65 TRP cc_start: 0.9109 (p90) cc_final: 0.8803 (p90) REVERT: C 133 ARG cc_start: 0.7475 (ttp-110) cc_final: 0.6781 (ttp-110) REVERT: C 231 LEU cc_start: 0.8987 (mt) cc_final: 0.8651 (mt) REVERT: C 252 TYR cc_start: 0.9178 (t80) cc_final: 0.8836 (t80) REVERT: C 256 LEU cc_start: 0.9368 (mm) cc_final: 0.9116 (mm) REVERT: C 287 TYR cc_start: 0.9162 (t80) cc_final: 0.8562 (t80) REVERT: C 301 MET cc_start: 0.8919 (mmp) cc_final: 0.8718 (ppp) REVERT: C 435 ILE cc_start: 0.9106 (pt) cc_final: 0.8860 (tp) REVERT: D 58 HIS cc_start: 0.9102 (m90) cc_final: 0.8897 (m-70) REVERT: D 103 PHE cc_start: 0.8724 (m-80) cc_final: 0.8186 (m-80) REVERT: D 155 VAL cc_start: 0.8810 (p) cc_final: 0.8443 (p) REVERT: D 287 TYR cc_start: 0.9307 (t80) cc_final: 0.8620 (t80) REVERT: D 295 ASN cc_start: 0.9115 (p0) cc_final: 0.8750 (p0) REVERT: D 301 MET cc_start: 0.8686 (tpt) cc_final: 0.8269 (mmm) REVERT: D 425 PHE cc_start: 0.8631 (t80) cc_final: 0.8377 (t80) REVERT: E 74 GLN cc_start: 0.8549 (mp10) cc_final: 0.8306 (mp10) REVERT: E 196 GLN cc_start: 0.9112 (tp40) cc_final: 0.8630 (tp40) REVERT: E 215 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8145 (mmmm) REVERT: E 235 LEU cc_start: 0.9450 (mt) cc_final: 0.9043 (mm) REVERT: E 238 LEU cc_start: 0.8927 (mp) cc_final: 0.8626 (mp) REVERT: E 252 TYR cc_start: 0.9260 (t80) cc_final: 0.8460 (t80) REVERT: E 256 LEU cc_start: 0.9394 (mm) cc_final: 0.9017 (mm) REVERT: E 266 MET cc_start: 0.8958 (ppp) cc_final: 0.8162 (ppp) REVERT: E 287 TYR cc_start: 0.9022 (t80) cc_final: 0.8670 (t80) REVERT: E 291 MET cc_start: 0.9296 (tpp) cc_final: 0.8838 (mmt) REVERT: E 296 LEU cc_start: 0.9448 (mt) cc_final: 0.9215 (mt) REVERT: E 301 MET cc_start: 0.8326 (mmm) cc_final: 0.8117 (mmm) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.1930 time to fit residues: 126.6632 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 : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 134 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12848 Z= 0.218 Angle : 0.702 10.764 17633 Z= 0.346 Chirality : 0.047 0.208 2167 Planarity : 0.003 0.033 2122 Dihedral : 5.665 55.491 1855 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: 1.31 (0.22), residues: 525 sheet: -0.77 (0.27), residues: 410 loop : -1.26 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 77 HIS 0.005 0.001 HIS C 161 PHE 0.023 0.002 PHE E 234 TYR 0.030 0.002 TYR D 252 ARG 0.006 0.000 ARG C 171 *********************** 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 417 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 2.917 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 58 HIS cc_start: 0.9041 (m-70) cc_final: 0.8625 (m-70) REVERT: A 72 ASP cc_start: 0.8464 (t70) cc_final: 0.7786 (t0) REVERT: A 103 PHE cc_start: 0.8549 (m-80) cc_final: 0.8259 (m-80) REVERT: A 125 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8511 (ttpp) REVERT: A 140 LEU cc_start: 0.9152 (mp) cc_final: 0.8815 (mt) REVERT: A 173 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8392 (tp-100) REVERT: A 234 PHE cc_start: 0.9093 (t80) cc_final: 0.8540 (t80) REVERT: A 265 MET cc_start: 0.8615 (ttt) cc_final: 0.8151 (ttm) REVERT: A 287 TYR cc_start: 0.9053 (t80) cc_final: 0.8017 (t80) REVERT: A 291 MET cc_start: 0.9242 (ttm) cc_final: 0.8880 (ttm) REVERT: A 296 LEU cc_start: 0.9172 (mt) cc_final: 0.8903 (mt) REVERT: B 72 ASP cc_start: 0.8340 (t70) cc_final: 0.7960 (t0) REVERT: B 252 TYR cc_start: 0.9128 (t80) cc_final: 0.8849 (t80) REVERT: B 256 LEU cc_start: 0.9475 (mm) cc_final: 0.9063 (mm) REVERT: B 266 MET cc_start: 0.8961 (ppp) cc_final: 0.8653 (ppp) REVERT: B 269 ASP cc_start: 0.7875 (m-30) cc_final: 0.7647 (m-30) REVERT: B 287 TYR cc_start: 0.8889 (t80) cc_final: 0.8449 (t80) REVERT: B 296 LEU cc_start: 0.9184 (mt) cc_final: 0.8913 (mt) REVERT: B 301 MET cc_start: 0.9095 (mmp) cc_final: 0.8466 (ptm) REVERT: C 58 HIS cc_start: 0.8839 (m-70) cc_final: 0.8448 (m-70) REVERT: C 65 TRP cc_start: 0.9098 (p90) cc_final: 0.8800 (p90) REVERT: C 77 TRP cc_start: 0.7142 (p-90) cc_final: 0.6844 (p-90) REVERT: C 133 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.6775 (ttp-110) REVERT: C 231 LEU cc_start: 0.8989 (mt) cc_final: 0.8677 (mt) REVERT: C 239 MET cc_start: 0.8799 (ttt) cc_final: 0.8247 (ttt) REVERT: C 252 TYR cc_start: 0.9177 (t80) cc_final: 0.8817 (t80) REVERT: C 256 LEU cc_start: 0.9443 (mm) cc_final: 0.9128 (mm) REVERT: C 287 TYR cc_start: 0.9159 (t80) cc_final: 0.8564 (t80) REVERT: C 301 MET cc_start: 0.8942 (mmp) cc_final: 0.8740 (ppp) REVERT: C 435 ILE cc_start: 0.9065 (pt) cc_final: 0.8805 (tp) REVERT: D 103 PHE cc_start: 0.8746 (m-80) cc_final: 0.8170 (m-80) REVERT: D 184 GLU cc_start: 0.8776 (pm20) cc_final: 0.8549 (pm20) REVERT: D 215 LYS cc_start: 0.8717 (tptm) cc_final: 0.8286 (mmmm) REVERT: D 266 MET cc_start: 0.8911 (ptm) cc_final: 0.8691 (ptt) REVERT: D 287 TYR cc_start: 0.9319 (t80) cc_final: 0.8641 (t80) REVERT: D 295 ASN cc_start: 0.9099 (p0) cc_final: 0.8745 (p0) REVERT: D 301 MET cc_start: 0.8668 (tpt) cc_final: 0.8255 (mmm) REVERT: D 425 PHE cc_start: 0.8622 (t80) cc_final: 0.8365 (t80) REVERT: E 74 GLN cc_start: 0.8483 (mp10) cc_final: 0.8245 (mp10) REVERT: E 184 GLU cc_start: 0.8780 (pm20) cc_final: 0.8551 (pm20) REVERT: E 196 GLN cc_start: 0.9107 (tp40) cc_final: 0.8627 (tp40) REVERT: E 215 LYS cc_start: 0.8418 (mmmm) cc_final: 0.7925 (mmmm) REVERT: E 235 LEU cc_start: 0.9452 (mt) cc_final: 0.9040 (mm) REVERT: E 238 LEU cc_start: 0.8986 (mp) cc_final: 0.8686 (mp) REVERT: E 252 TYR cc_start: 0.9247 (t80) cc_final: 0.8438 (t80) REVERT: E 256 LEU cc_start: 0.9379 (mm) cc_final: 0.8999 (mm) REVERT: E 266 MET cc_start: 0.8953 (ppp) cc_final: 0.8115 (ppp) REVERT: E 287 TYR cc_start: 0.9024 (t80) cc_final: 0.8657 (t80) REVERT: E 291 MET cc_start: 0.9328 (tpp) cc_final: 0.8739 (mmt) REVERT: E 296 LEU cc_start: 0.9445 (mt) cc_final: 0.9226 (mt) REVERT: E 301 MET cc_start: 0.8308 (mmm) cc_final: 0.8097 (mmm) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2270 time to fit residues: 149.0236 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 : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 105 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN B 40 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12848 Z= 0.192 Angle : 0.710 11.158 17633 Z= 0.348 Chirality : 0.046 0.207 2167 Planarity : 0.004 0.035 2122 Dihedral : 5.633 55.640 1855 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.27 % Rotamer: Outliers : 0.16 % Allowed : 0.56 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.21), residues: 1610 helix: 1.27 (0.23), residues: 525 sheet: -0.76 (0.26), residues: 430 loop : -1.25 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 65 HIS 0.005 0.001 HIS E 131 PHE 0.038 0.002 PHE D 289 TYR 0.032 0.001 TYR D 252 ARG 0.006 0.000 ARG C 171 ********************** 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 423 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 421 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.9037 (m-70) cc_final: 0.8603 (m-70) REVERT: A 72 ASP cc_start: 0.8439 (t70) cc_final: 0.7772 (t0) REVERT: A 103 PHE cc_start: 0.8490 (m-80) cc_final: 0.8177 (m-80) REVERT: A 125 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8495 (ttpp) REVERT: A 140 LEU cc_start: 0.9122 (mp) cc_final: 0.8750 (mt) REVERT: A 173 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8363 (tp-100) REVERT: A 234 PHE cc_start: 0.9088 (t80) cc_final: 0.8553 (t80) REVERT: A 287 TYR cc_start: 0.9024 (t80) cc_final: 0.8007 (t80) REVERT: A 291 MET cc_start: 0.9287 (ttm) cc_final: 0.9017 (ttm) REVERT: A 296 LEU cc_start: 0.9175 (mt) cc_final: 0.8889 (mt) REVERT: B 69 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 85 LEU cc_start: 0.9081 (tp) cc_final: 0.8787 (pp) REVERT: B 227 MET cc_start: 0.8270 (tpp) cc_final: 0.8052 (tpp) REVERT: B 252 TYR cc_start: 0.9105 (t80) cc_final: 0.8775 (t80) REVERT: B 256 LEU cc_start: 0.9489 (mm) cc_final: 0.9049 (mm) REVERT: B 266 MET cc_start: 0.9043 (ppp) cc_final: 0.8669 (ppp) REVERT: B 287 TYR cc_start: 0.8855 (t80) cc_final: 0.8449 (t80) REVERT: B 296 LEU cc_start: 0.9081 (mt) cc_final: 0.8805 (mt) REVERT: B 301 MET cc_start: 0.9079 (mmp) cc_final: 0.8464 (ptm) REVERT: C 58 HIS cc_start: 0.8818 (m-70) cc_final: 0.8495 (m-70) REVERT: C 65 TRP cc_start: 0.9095 (p90) cc_final: 0.8781 (p90) REVERT: C 77 TRP cc_start: 0.7122 (p-90) cc_final: 0.6839 (p-90) REVERT: C 133 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.6849 (ttp-110) REVERT: C 231 LEU cc_start: 0.8973 (mt) cc_final: 0.8669 (mt) REVERT: C 252 TYR cc_start: 0.9151 (t80) cc_final: 0.8726 (t80) REVERT: C 256 LEU cc_start: 0.9396 (mm) cc_final: 0.9104 (mm) REVERT: C 287 TYR cc_start: 0.9143 (t80) cc_final: 0.8548 (t80) REVERT: C 435 ILE cc_start: 0.9025 (pt) cc_final: 0.8761 (tp) REVERT: D 58 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8742 (m-70) REVERT: D 103 PHE cc_start: 0.8737 (m-80) cc_final: 0.8091 (m-80) REVERT: D 155 VAL cc_start: 0.8840 (p) cc_final: 0.8538 (p) REVERT: D 184 GLU cc_start: 0.8759 (pm20) cc_final: 0.8517 (pm20) REVERT: D 215 LYS cc_start: 0.8656 (tptm) cc_final: 0.8213 (mmmm) REVERT: D 287 TYR cc_start: 0.9262 (t80) cc_final: 0.8584 (t80) REVERT: D 295 ASN cc_start: 0.9086 (p0) cc_final: 0.8736 (p0) REVERT: D 301 MET cc_start: 0.8558 (tpt) cc_final: 0.8077 (mmm) REVERT: D 425 PHE cc_start: 0.8577 (t80) cc_final: 0.8302 (t80) REVERT: E 74 GLN cc_start: 0.8502 (mp10) cc_final: 0.8264 (mp10) REVERT: E 129 VAL cc_start: 0.9554 (t) cc_final: 0.9334 (t) REVERT: E 196 GLN cc_start: 0.9104 (tp40) cc_final: 0.8630 (tp40) REVERT: E 215 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7906 (mmmm) REVERT: E 235 LEU cc_start: 0.9401 (mt) cc_final: 0.8986 (mm) REVERT: E 238 LEU cc_start: 0.9030 (mp) cc_final: 0.8734 (mp) REVERT: E 252 TYR cc_start: 0.9229 (t80) cc_final: 0.8421 (t80) REVERT: E 256 LEU cc_start: 0.9362 (mm) cc_final: 0.8975 (mm) REVERT: E 266 MET cc_start: 0.8927 (ppp) cc_final: 0.8167 (ppp) REVERT: E 287 TYR cc_start: 0.9030 (t80) cc_final: 0.8639 (t80) REVERT: E 291 MET cc_start: 0.9346 (tpp) cc_final: 0.8780 (mmt) REVERT: E 296 LEU cc_start: 0.9437 (mt) cc_final: 0.9225 (mt) REVERT: E 301 MET cc_start: 0.8283 (mmm) cc_final: 0.8077 (mmm) outliers start: 2 outliers final: 0 residues processed: 421 average time/residue: 0.1931 time to fit residues: 125.4050 Evaluate side-chains 372 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 371 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN B 40 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082305 restraints weight = 37561.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085076 restraints weight = 23927.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087031 restraints weight = 17257.693| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12848 Z= 0.199 Angle : 0.712 14.042 17633 Z= 0.347 Chirality : 0.046 0.207 2167 Planarity : 0.003 0.034 2122 Dihedral : 5.545 54.725 1855 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 0.16 % Allowed : 0.56 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.22), residues: 525 sheet: -0.84 (0.26), residues: 445 loop : -1.16 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 65 HIS 0.004 0.001 HIS E 131 PHE 0.023 0.002 PHE E 234 TYR 0.033 0.001 TYR D 252 ARG 0.005 0.000 ARG C 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.16 seconds wall clock time: 55 minutes 1.87 seconds (3301.87 seconds total)