Starting phenix.real_space_refine on Fri Oct 10 20:00:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dw1_8923/10_2025/6dw1_8923.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dw1_8923/10_2025/6dw1_8923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dw1_8923/10_2025/6dw1_8923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dw1_8923/10_2025/6dw1_8923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dw1_8923/10_2025/6dw1_8923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dw1_8923/10_2025/6dw1_8923.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 45 5.16 5 C 5461 2.51 5 N 1443 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8595 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1612 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 199} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1673 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1672 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 198} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1685 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ABU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.29, per 1000 atoms: 0.27 Number of scatterers: 8595 At special positions: 0 Unit cell: (90.86, 95.403, 86.966, 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 45 16.00 O 1646 8.00 N 1443 7.00 C 5461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 165 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG F 1 " - " ASN C 110 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN E 149 " " NAG I 1 " - " ASN E 80 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 80 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 353.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 21 sheets defined 9.8% alpha, 53.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'D' and resid 25 through 33 removed outlier: 3.575A pdb=" N ILE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 88 removed outlier: 3.847A pdb=" N LYS D 88 " --> pdb=" O ARG D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 88' Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.672A pdb=" N ILE C 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.821A pdb=" N SER C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.615A pdb=" N ASP A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.773A pdb=" N LYS A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.705A pdb=" N ALA A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 141 through 145 removed outlier: 4.427A pdb=" N ASP A 144 " --> pdb=" O HIS A 141 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 145' Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.556A pdb=" N THR E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.916A pdb=" N SER E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.760A pdb=" N ALA E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'B' and resid 9 through 21 removed outlier: 3.555A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 177 through 181 Processing sheet with id=AA1, first strand: chain 'D' and resid 95 through 98 removed outlier: 3.661A pdb=" N LEU D 131 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG D 138 " --> pdb=" O TRP D 134 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR D 72 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU D 71 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP D 75 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR D 83 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU D 52 " --> pdb=" O TYR D 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.815A pdb=" N TYR D 72 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU D 71 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP D 75 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR D 83 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU D 52 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N GLY D 191 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET D 57 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AA4, first strand: chain 'D' and resid 166 through 167 removed outlier: 3.597A pdb=" N ARG D 207 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY D 205 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 211 through 214 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.797A pdb=" N THR C 60 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE C 49 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP C 62 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.797A pdb=" N THR C 60 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE C 49 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP C 62 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 82 through 85 removed outlier: 4.265A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.587A pdb=" N GLY C 194 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS C 219 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU C 192 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB2, first strand: chain 'A' and resid 46 through 53 removed outlier: 7.263A pdb=" N THR A 47 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N PHE A 64 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE A 49 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP A 62 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 60 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP A 69 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 46 through 53 removed outlier: 7.263A pdb=" N THR A 47 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N PHE A 64 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE A 49 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP A 62 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 60 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 70 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A 39 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.168A pdb=" N SER A 158 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 210 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.168A pdb=" N SER A 158 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 210 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 194 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS A 219 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 192 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 103 through 106 removed outlier: 4.408A pdb=" N LYS A 105 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.530A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 68 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP E 37 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.110A pdb=" N ASP E 101 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA E 135 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 103 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 105 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 68 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP E 37 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.889A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS E 192 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.755A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B 68 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 37 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.433A pdb=" N ASP B 101 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA B 135 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 103 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B 68 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 37 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR B 176 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 42 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.763A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2705 1.34 - 1.46: 2077 1.46 - 1.58: 3921 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 8783 Sorted by residual: bond pdb=" C PHE C 145 " pdb=" N PRO C 146 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " ideal model delta sigma weight residual 1.524 1.575 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 5.00e+00 bond pdb=" C5 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 MAN G 7 " pdb=" O5 MAN G 7 " ideal model delta sigma weight residual 1.399 1.440 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 8778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 11658 2.75 - 5.51: 211 5.51 - 8.26: 48 8.26 - 11.01: 4 11.01 - 13.77: 1 Bond angle restraints: 11922 Sorted by residual: angle pdb=" N PRO D 127 " pdb=" CA PRO D 127 " pdb=" C PRO D 127 " ideal model delta sigma weight residual 112.47 121.32 -8.85 2.06e+00 2.36e-01 1.84e+01 angle pdb=" C ASP A 144 " pdb=" N PHE A 145 " pdb=" CA PHE A 145 " ideal model delta sigma weight residual 120.58 126.06 -5.48 1.32e+00 5.74e-01 1.72e+01 angle pdb=" C ILE E 47 " pdb=" N ASP E 48 " pdb=" CA ASP E 48 " ideal model delta sigma weight residual 121.19 127.49 -6.30 1.59e+00 3.96e-01 1.57e+01 angle pdb=" CA LEU E 145 " pdb=" CB LEU E 145 " pdb=" CG LEU E 145 " ideal model delta sigma weight residual 116.30 130.07 -13.77 3.50e+00 8.16e-02 1.55e+01 angle pdb=" N ASP E 48 " pdb=" CA ASP E 48 " pdb=" C ASP E 48 " ideal model delta sigma weight residual 111.37 117.59 -6.22 1.64e+00 3.72e-01 1.44e+01 ... (remaining 11917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.27: 5235 23.27 - 46.55: 151 46.55 - 69.82: 37 69.82 - 93.09: 40 93.09 - 116.36: 43 Dihedral angle restraints: 5506 sinusoidal: 2445 harmonic: 3061 Sorted by residual: dihedral pdb=" CA THR D 126 " pdb=" C THR D 126 " pdb=" N PRO D 127 " pdb=" CA PRO D 127 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 50.43 42.57 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CA THR C 112 " pdb=" C THR C 112 " pdb=" N MET C 113 " pdb=" CA MET C 113 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 5503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1216 0.080 - 0.160: 168 0.160 - 0.241: 13 0.241 - 0.321: 4 0.321 - 0.401: 2 Chirality restraints: 1403 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C1 MAN G 6 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 6 " pdb=" O5 MAN G 6 " both_signs ideal model delta sigma weight residual False 2.40 2.36 0.04 2.00e-02 2.50e+03 3.08e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1400 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 143 " -0.050 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO E 144 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 49 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO D 50 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 145 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 146 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.032 5.00e-02 4.00e+02 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2533 2.82 - 3.34: 6977 3.34 - 3.86: 14269 3.86 - 4.38: 16119 4.38 - 4.90: 28635 Nonbonded interactions: 68533 Sorted by model distance: nonbonded pdb=" OG1 THR A 98 " pdb=" OH TYR A 168 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR B 57 " pdb=" O THR B 151 " model vdw 2.315 3.040 nonbonded pdb=" NH1 ARG D 129 " pdb=" OH TYR D 141 " model vdw 2.334 3.120 nonbonded pdb=" OG SER B 46 " pdb=" OD1 ASP B 48 " model vdw 2.343 3.040 nonbonded pdb=" OD1 ASP E 146 " pdb=" NH1 ARG E 216 " model vdw 2.351 3.120 ... (remaining 68528 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 70 or (resid 71 through 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 76 or (resid 77 and (na \ me N or name CA or name C or name O or name CB )) or resid 78 through 79 or (res \ id 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 408)) selection = (chain 'C' and (resid 12 through 34 or (resid 35 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 86 or (res \ id 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 174 through 405)) } ncs_group { reference = (chain 'B' and (resid 10 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 191 or (resid 192 and (name N or n \ ame CA or name C or name O or name CB )) or resid 193 through 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 10 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 29 or (resid 30 and (name N or nam \ e CA or name C or name O or name CB )) or resid 31 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 through 138 or ( \ resid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 \ through 217)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.006 0.072 8809 Z= 0.264 Angle : 0.988 13.768 11995 Z= 0.488 Chirality : 0.058 0.401 1403 Planarity : 0.006 0.075 1483 Dihedral : 18.013 116.363 3523 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.22), residues: 1036 helix: -4.69 (0.23), residues: 62 sheet: -2.08 (0.24), residues: 371 loop : -2.49 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 131 TYR 0.018 0.002 TYR C 168 PHE 0.026 0.003 PHE A 99 TRP 0.026 0.003 TRP A 94 HIS 0.011 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 8783) covalent geometry : angle 0.97228 (11922) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.92897 ( 10) hydrogen bonds : bond 0.25799 ( 249) hydrogen bonds : angle 10.48460 ( 939) link_ALPHA1-2 : bond 0.00142 ( 1) link_ALPHA1-2 : angle 2.40614 ( 3) link_ALPHA1-3 : bond 0.00600 ( 3) link_ALPHA1-3 : angle 2.37765 ( 9) link_ALPHA1-6 : bond 0.00575 ( 1) link_ALPHA1-6 : angle 2.41993 ( 3) link_BETA1-4 : bond 0.00820 ( 10) link_BETA1-4 : angle 2.20384 ( 30) link_NAG-ASN : bond 0.00488 ( 6) link_NAG-ASN : angle 3.28192 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8391 (mttt) cc_final: 0.8013 (tmtt) REVERT: C 113 MET cc_start: 0.8047 (mmm) cc_final: 0.7779 (mmt) REVERT: A 17 ILE cc_start: 0.8896 (tp) cc_final: 0.8545 (mt) REVERT: A 59 TYR cc_start: 0.9130 (p90) cc_final: 0.8881 (p90) REVERT: E 47 ILE cc_start: 0.9070 (mm) cc_final: 0.8679 (mm) REVERT: E 180 LYS cc_start: 0.8996 (mptt) cc_final: 0.8690 (mtpt) REVERT: B 142 ARG cc_start: 0.6989 (pmm-80) cc_final: 0.6661 (ptm160) REVERT: B 160 THR cc_start: 0.8652 (m) cc_final: 0.8448 (p) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1194 time to fit residues: 43.5195 Evaluate side-chains 172 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 101 HIS ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN B 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097422 restraints weight = 17001.851| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.61 r_work: 0.3315 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8809 Z= 0.132 Angle : 0.738 8.678 11995 Z= 0.359 Chirality : 0.048 0.218 1403 Planarity : 0.005 0.059 1483 Dihedral : 16.640 100.114 1595 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.46 % Allowed : 11.51 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.24), residues: 1036 helix: -3.23 (0.42), residues: 62 sheet: -1.59 (0.23), residues: 425 loop : -1.98 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 114 TYR 0.015 0.001 TYR D 141 PHE 0.020 0.002 PHE C 64 TRP 0.012 0.001 TRP A 94 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8783) covalent geometry : angle 0.71982 (11922) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.41733 ( 10) hydrogen bonds : bond 0.04073 ( 249) hydrogen bonds : angle 6.57759 ( 939) link_ALPHA1-2 : bond 0.00596 ( 1) link_ALPHA1-2 : angle 1.90969 ( 3) link_ALPHA1-3 : bond 0.00866 ( 3) link_ALPHA1-3 : angle 1.62491 ( 9) link_ALPHA1-6 : bond 0.00537 ( 1) link_ALPHA1-6 : angle 3.47777 ( 3) link_BETA1-4 : bond 0.00508 ( 10) link_BETA1-4 : angle 2.67063 ( 30) link_NAG-ASN : bond 0.00461 ( 6) link_NAG-ASN : angle 1.95850 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8445 (mttt) cc_final: 0.7857 (tmtt) REVERT: C 75 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8057 (mmtp) REVERT: C 212 MET cc_start: 0.8477 (mmm) cc_final: 0.7743 (mmm) REVERT: A 39 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 59 TYR cc_start: 0.9181 (p90) cc_final: 0.8886 (p90) REVERT: E 47 ILE cc_start: 0.9146 (mm) cc_final: 0.8773 (mm) REVERT: E 103 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8148 (mtmm) REVERT: E 143 TYR cc_start: 0.8114 (t80) cc_final: 0.7111 (m-80) REVERT: B 49 MET cc_start: 0.6550 (tmm) cc_final: 0.6267 (mtt) REVERT: B 142 ARG cc_start: 0.7335 (pmm-80) cc_final: 0.6471 (ptm160) outliers start: 22 outliers final: 10 residues processed: 208 average time/residue: 0.0971 time to fit residues: 27.7009 Evaluate side-chains 174 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain B residue 152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 195 GLN E 64 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096660 restraints weight = 16836.685| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.50 r_work: 0.3309 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 0.044 8809 Z= 0.128 Angle : 0.690 8.177 11995 Z= 0.332 Chirality : 0.047 0.239 1403 Planarity : 0.004 0.052 1483 Dihedral : 12.154 92.583 1595 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.24 % Allowed : 11.62 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.25), residues: 1036 helix: -2.46 (0.53), residues: 64 sheet: -1.40 (0.24), residues: 437 loop : -1.64 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 172 TYR 0.013 0.001 TYR E 126 PHE 0.024 0.001 PHE C 64 TRP 0.010 0.001 TRP B 92 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8783) covalent geometry : angle 0.67313 (11922) SS BOND : bond 0.00131 ( 5) SS BOND : angle 0.33984 ( 10) hydrogen bonds : bond 0.03365 ( 249) hydrogen bonds : angle 5.77271 ( 939) link_ALPHA1-2 : bond 0.01173 ( 1) link_ALPHA1-2 : angle 1.45740 ( 3) link_ALPHA1-3 : bond 0.00783 ( 3) link_ALPHA1-3 : angle 1.48876 ( 9) link_ALPHA1-6 : bond 0.00614 ( 1) link_ALPHA1-6 : angle 3.09456 ( 3) link_BETA1-4 : bond 0.00592 ( 10) link_BETA1-4 : angle 2.57348 ( 30) link_NAG-ASN : bond 0.00406 ( 6) link_NAG-ASN : angle 1.78131 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8443 (mttt) cc_final: 0.7853 (tmtt) REVERT: D 224 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8544 (p) REVERT: C 106 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8715 (p) REVERT: C 212 MET cc_start: 0.8404 (mmm) cc_final: 0.7727 (mmm) REVERT: A 27 ASN cc_start: 0.8240 (t0) cc_final: 0.7958 (t0) REVERT: A 59 TYR cc_start: 0.9164 (p90) cc_final: 0.8845 (p90) REVERT: E 47 ILE cc_start: 0.9162 (mm) cc_final: 0.8718 (mm) REVERT: E 103 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8144 (mtmm) REVERT: E 143 TYR cc_start: 0.8017 (t80) cc_final: 0.7039 (m-80) REVERT: B 49 MET cc_start: 0.6635 (tmm) cc_final: 0.6368 (mtt) REVERT: B 142 ARG cc_start: 0.7460 (pmm-80) cc_final: 0.6625 (ptm160) outliers start: 29 outliers final: 19 residues processed: 186 average time/residue: 0.0938 time to fit residues: 24.2838 Evaluate side-chains 182 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.103575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088785 restraints weight = 17493.021| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.57 r_work: 0.3159 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 8809 Z= 0.348 Angle : 0.841 11.547 11995 Z= 0.412 Chirality : 0.052 0.260 1403 Planarity : 0.006 0.062 1483 Dihedral : 10.428 71.693 1595 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 5.25 % Allowed : 12.29 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.25), residues: 1036 helix: -2.11 (0.57), residues: 71 sheet: -1.34 (0.23), residues: 442 loop : -1.57 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 172 TYR 0.019 0.002 TYR E 126 PHE 0.020 0.003 PHE E 212 TRP 0.015 0.002 TRP A 94 HIS 0.008 0.002 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00803 ( 8783) covalent geometry : angle 0.82215 (11922) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.67065 ( 10) hydrogen bonds : bond 0.03794 ( 249) hydrogen bonds : angle 6.03283 ( 939) link_ALPHA1-2 : bond 0.00655 ( 1) link_ALPHA1-2 : angle 1.42880 ( 3) link_ALPHA1-3 : bond 0.00503 ( 3) link_ALPHA1-3 : angle 2.20730 ( 9) link_ALPHA1-6 : bond 0.00562 ( 1) link_ALPHA1-6 : angle 3.89566 ( 3) link_BETA1-4 : bond 0.00696 ( 10) link_BETA1-4 : angle 2.85966 ( 30) link_NAG-ASN : bond 0.00534 ( 6) link_NAG-ASN : angle 2.17292 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8721 (mttt) cc_final: 0.8098 (tmtt) REVERT: C 212 MET cc_start: 0.8461 (mmm) cc_final: 0.7831 (mmm) REVERT: A 59 TYR cc_start: 0.9203 (p90) cc_final: 0.8854 (p90) REVERT: E 47 ILE cc_start: 0.9161 (mm) cc_final: 0.8806 (mm) REVERT: E 143 TYR cc_start: 0.8165 (t80) cc_final: 0.7104 (m-80) REVERT: B 49 MET cc_start: 0.7164 (tmm) cc_final: 0.6831 (tmm) REVERT: B 142 ARG cc_start: 0.8066 (pmm-80) cc_final: 0.7056 (ptm160) outliers start: 47 outliers final: 34 residues processed: 188 average time/residue: 0.0906 time to fit residues: 23.8163 Evaluate side-chains 181 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 195 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.108098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093217 restraints weight = 16962.161| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.56 r_work: 0.3247 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8809 Z= 0.117 Angle : 0.665 11.270 11995 Z= 0.325 Chirality : 0.045 0.267 1403 Planarity : 0.004 0.051 1483 Dihedral : 9.071 66.084 1595 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.46 % Allowed : 13.63 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.25), residues: 1036 helix: -1.67 (0.65), residues: 64 sheet: -1.10 (0.24), residues: 409 loop : -1.48 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 97 TYR 0.014 0.001 TYR E 126 PHE 0.012 0.001 PHE C 64 TRP 0.010 0.001 TRP D 123 HIS 0.003 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8783) covalent geometry : angle 0.65049 (11922) SS BOND : bond 0.00116 ( 5) SS BOND : angle 0.22999 ( 10) hydrogen bonds : bond 0.02842 ( 249) hydrogen bonds : angle 5.44538 ( 939) link_ALPHA1-2 : bond 0.00640 ( 1) link_ALPHA1-2 : angle 1.36198 ( 3) link_ALPHA1-3 : bond 0.01021 ( 3) link_ALPHA1-3 : angle 1.55214 ( 9) link_ALPHA1-6 : bond 0.01327 ( 1) link_ALPHA1-6 : angle 2.07584 ( 3) link_BETA1-4 : bond 0.00525 ( 10) link_BETA1-4 : angle 2.31848 ( 30) link_NAG-ASN : bond 0.00282 ( 6) link_NAG-ASN : angle 1.80533 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8343 (t0) cc_final: 0.8029 (t0) REVERT: D 214 LYS cc_start: 0.8566 (mttt) cc_final: 0.7873 (tmtt) REVERT: C 212 MET cc_start: 0.8344 (mmm) cc_final: 0.7784 (mmm) REVERT: A 62 ASP cc_start: 0.7227 (p0) cc_final: 0.6987 (p0) REVERT: E 47 ILE cc_start: 0.9089 (mm) cc_final: 0.8735 (mm) REVERT: E 143 TYR cc_start: 0.8101 (t80) cc_final: 0.7108 (m-80) REVERT: B 49 MET cc_start: 0.6959 (tmm) cc_final: 0.6514 (mtt) REVERT: B 142 ARG cc_start: 0.7932 (pmm-80) cc_final: 0.6967 (ptm160) outliers start: 31 outliers final: 20 residues processed: 191 average time/residue: 0.0950 time to fit residues: 24.9669 Evaluate side-chains 176 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 22 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN E 90 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093944 restraints weight = 16961.690| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.50 r_work: 0.3263 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8809 Z= 0.120 Angle : 0.643 10.205 11995 Z= 0.314 Chirality : 0.045 0.262 1403 Planarity : 0.004 0.051 1483 Dihedral : 8.082 58.900 1595 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.46 % Allowed : 14.30 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.26), residues: 1036 helix: -1.47 (0.66), residues: 64 sheet: -1.09 (0.24), residues: 425 loop : -1.21 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.019 0.001 TYR E 11 PHE 0.010 0.001 PHE C 64 TRP 0.007 0.001 TRP B 67 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8783) covalent geometry : angle 0.62831 (11922) SS BOND : bond 0.00336 ( 5) SS BOND : angle 0.27458 ( 10) hydrogen bonds : bond 0.02668 ( 249) hydrogen bonds : angle 5.13132 ( 939) link_ALPHA1-2 : bond 0.00648 ( 1) link_ALPHA1-2 : angle 1.45076 ( 3) link_ALPHA1-3 : bond 0.00914 ( 3) link_ALPHA1-3 : angle 1.59879 ( 9) link_ALPHA1-6 : bond 0.00874 ( 1) link_ALPHA1-6 : angle 1.89127 ( 3) link_BETA1-4 : bond 0.00563 ( 10) link_BETA1-4 : angle 2.24998 ( 30) link_NAG-ASN : bond 0.00296 ( 6) link_NAG-ASN : angle 1.75443 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8268 (t0) cc_final: 0.7971 (t0) REVERT: D 197 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5779 (ptt180) REVERT: D 214 LYS cc_start: 0.8530 (mttt) cc_final: 0.7891 (tmtt) REVERT: C 212 MET cc_start: 0.8328 (mmm) cc_final: 0.7770 (mmm) REVERT: E 47 ILE cc_start: 0.9107 (mm) cc_final: 0.8727 (mm) REVERT: E 103 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8223 (mtmm) REVERT: E 143 TYR cc_start: 0.8023 (t80) cc_final: 0.7060 (m-80) REVERT: B 49 MET cc_start: 0.6933 (tmm) cc_final: 0.6516 (tmm) REVERT: B 90 GLN cc_start: 0.8222 (mm-40) cc_final: 0.8013 (mm-40) REVERT: B 142 ARG cc_start: 0.7947 (pmm-80) cc_final: 0.7021 (ptm160) outliers start: 31 outliers final: 27 residues processed: 177 average time/residue: 0.0928 time to fit residues: 22.7973 Evaluate side-chains 186 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093323 restraints weight = 17045.909| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.57 r_work: 0.3250 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8809 Z= 0.139 Angle : 0.651 9.273 11995 Z= 0.318 Chirality : 0.045 0.254 1403 Planarity : 0.004 0.051 1483 Dihedral : 7.514 53.145 1595 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.91 % Allowed : 14.86 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.26), residues: 1036 helix: -1.54 (0.65), residues: 66 sheet: -1.10 (0.23), residues: 444 loop : -1.15 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.026 0.001 TYR E 11 PHE 0.010 0.001 PHE E 212 TRP 0.011 0.001 TRP D 123 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8783) covalent geometry : angle 0.63654 (11922) SS BOND : bond 0.00089 ( 5) SS BOND : angle 0.48281 ( 10) hydrogen bonds : bond 0.02659 ( 249) hydrogen bonds : angle 5.05876 ( 939) link_ALPHA1-2 : bond 0.00605 ( 1) link_ALPHA1-2 : angle 1.46696 ( 3) link_ALPHA1-3 : bond 0.00910 ( 3) link_ALPHA1-3 : angle 1.57918 ( 9) link_ALPHA1-6 : bond 0.00560 ( 1) link_ALPHA1-6 : angle 2.16355 ( 3) link_BETA1-4 : bond 0.00561 ( 10) link_BETA1-4 : angle 2.25996 ( 30) link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 1.76124 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8271 (t0) cc_final: 0.7982 (t0) REVERT: D 197 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5802 (ptt180) REVERT: D 214 LYS cc_start: 0.8552 (mttt) cc_final: 0.7915 (tmtt) REVERT: C 212 MET cc_start: 0.8352 (mmm) cc_final: 0.7802 (mmm) REVERT: A 89 MET cc_start: 0.8752 (tpt) cc_final: 0.8466 (tpp) REVERT: E 47 ILE cc_start: 0.9094 (mm) cc_final: 0.8703 (mm) REVERT: E 103 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8218 (mtmm) REVERT: E 143 TYR cc_start: 0.8031 (t80) cc_final: 0.7060 (m-80) REVERT: B 49 MET cc_start: 0.6984 (tmm) cc_final: 0.6527 (tmm) REVERT: B 142 ARG cc_start: 0.8028 (pmm-80) cc_final: 0.7044 (ptm160) REVERT: B 212 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7244 (p90) outliers start: 35 outliers final: 28 residues processed: 176 average time/residue: 0.0941 time to fit residues: 23.1798 Evaluate side-chains 184 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093934 restraints weight = 16767.134| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.57 r_work: 0.3261 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8809 Z= 0.129 Angle : 0.647 8.889 11995 Z= 0.317 Chirality : 0.044 0.233 1403 Planarity : 0.004 0.049 1483 Dihedral : 6.870 45.965 1595 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.02 % Allowed : 15.20 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.26), residues: 1036 helix: -1.50 (0.65), residues: 66 sheet: -1.04 (0.24), residues: 439 loop : -1.17 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.017 0.001 TYR A 59 PHE 0.009 0.001 PHE E 212 TRP 0.019 0.001 TRP D 123 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8783) covalent geometry : angle 0.63327 (11922) SS BOND : bond 0.00109 ( 5) SS BOND : angle 0.35736 ( 10) hydrogen bonds : bond 0.02568 ( 249) hydrogen bonds : angle 4.96035 ( 939) link_ALPHA1-2 : bond 0.00597 ( 1) link_ALPHA1-2 : angle 1.53281 ( 3) link_ALPHA1-3 : bond 0.00858 ( 3) link_ALPHA1-3 : angle 1.54431 ( 9) link_ALPHA1-6 : bond 0.00459 ( 1) link_ALPHA1-6 : angle 2.15926 ( 3) link_BETA1-4 : bond 0.00528 ( 10) link_BETA1-4 : angle 2.22163 ( 30) link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 1.75373 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8260 (t0) cc_final: 0.7973 (t0) REVERT: D 197 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5779 (ptt180) REVERT: D 214 LYS cc_start: 0.8520 (mttt) cc_final: 0.7923 (tmtt) REVERT: C 212 MET cc_start: 0.8343 (mmm) cc_final: 0.7748 (mmm) REVERT: A 89 MET cc_start: 0.8744 (tpt) cc_final: 0.8473 (tpp) REVERT: E 47 ILE cc_start: 0.9094 (mm) cc_final: 0.8696 (mm) REVERT: E 103 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8189 (mtmm) REVERT: E 143 TYR cc_start: 0.8015 (t80) cc_final: 0.7064 (m-80) REVERT: B 49 MET cc_start: 0.6968 (tmm) cc_final: 0.6493 (tmm) REVERT: B 142 ARG cc_start: 0.8070 (pmm-80) cc_final: 0.7085 (ptm160) REVERT: B 212 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7259 (p90) outliers start: 36 outliers final: 25 residues processed: 189 average time/residue: 0.0971 time to fit residues: 25.1620 Evaluate side-chains 187 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 4 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096438 restraints weight = 16862.638| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.50 r_work: 0.3305 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8809 Z= 0.103 Angle : 0.637 10.267 11995 Z= 0.311 Chirality : 0.044 0.192 1403 Planarity : 0.004 0.049 1483 Dihedral : 6.150 37.604 1595 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.57 % Allowed : 16.20 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.26), residues: 1036 helix: -1.39 (0.64), residues: 66 sheet: -0.91 (0.24), residues: 436 loop : -1.06 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.020 0.001 TYR E 11 PHE 0.010 0.001 PHE C 64 TRP 0.018 0.001 TRP D 123 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8783) covalent geometry : angle 0.62387 (11922) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.34385 ( 10) hydrogen bonds : bond 0.02499 ( 249) hydrogen bonds : angle 4.77749 ( 939) link_ALPHA1-2 : bond 0.00577 ( 1) link_ALPHA1-2 : angle 1.56146 ( 3) link_ALPHA1-3 : bond 0.00801 ( 3) link_ALPHA1-3 : angle 1.53950 ( 9) link_ALPHA1-6 : bond 0.00599 ( 1) link_ALPHA1-6 : angle 1.79629 ( 3) link_BETA1-4 : bond 0.00582 ( 10) link_BETA1-4 : angle 2.15394 ( 30) link_NAG-ASN : bond 0.00312 ( 6) link_NAG-ASN : angle 1.64277 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8428 (mttt) cc_final: 0.7856 (tmtt) REVERT: C 212 MET cc_start: 0.8326 (mmm) cc_final: 0.7728 (mmm) REVERT: A 89 MET cc_start: 0.8746 (tpt) cc_final: 0.8478 (tpp) REVERT: A 140 MET cc_start: 0.8325 (tpp) cc_final: 0.7949 (mtt) REVERT: E 47 ILE cc_start: 0.9093 (mm) cc_final: 0.8697 (mm) REVERT: E 215 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6879 (ptmm) REVERT: B 49 MET cc_start: 0.6853 (tmm) cc_final: 0.6422 (tmm) REVERT: B 142 ARG cc_start: 0.7973 (pmm-80) cc_final: 0.7042 (ptm160) REVERT: B 185 GLN cc_start: 0.7548 (pt0) cc_final: 0.7090 (tt0) REVERT: B 212 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7290 (p90) outliers start: 23 outliers final: 18 residues processed: 184 average time/residue: 0.0966 time to fit residues: 24.4546 Evaluate side-chains 178 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093537 restraints weight = 16993.849| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.48 r_work: 0.3253 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8809 Z= 0.179 Angle : 0.672 9.415 11995 Z= 0.331 Chirality : 0.045 0.187 1403 Planarity : 0.004 0.051 1483 Dihedral : 6.184 34.685 1595 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.57 % Allowed : 17.32 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.26), residues: 1036 helix: -1.39 (0.64), residues: 66 sheet: -0.95 (0.23), residues: 439 loop : -1.10 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.044 0.002 TYR D 72 PHE 0.010 0.001 PHE A 64 TRP 0.018 0.001 TRP D 123 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8783) covalent geometry : angle 0.65816 (11922) SS BOND : bond 0.00462 ( 5) SS BOND : angle 0.61090 ( 10) hydrogen bonds : bond 0.02735 ( 249) hydrogen bonds : angle 5.02214 ( 939) link_ALPHA1-2 : bond 0.00566 ( 1) link_ALPHA1-2 : angle 1.61090 ( 3) link_ALPHA1-3 : bond 0.00760 ( 3) link_ALPHA1-3 : angle 1.62264 ( 9) link_ALPHA1-6 : bond 0.00269 ( 1) link_ALPHA1-6 : angle 2.41559 ( 3) link_BETA1-4 : bond 0.00487 ( 10) link_BETA1-4 : angle 2.18426 ( 30) link_NAG-ASN : bond 0.00257 ( 6) link_NAG-ASN : angle 1.70863 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8543 (mttt) cc_final: 0.7978 (tmtt) REVERT: C 212 MET cc_start: 0.8356 (mmm) cc_final: 0.7786 (mmm) REVERT: A 89 MET cc_start: 0.8676 (tpt) cc_final: 0.8437 (tpp) REVERT: E 47 ILE cc_start: 0.9052 (mm) cc_final: 0.8589 (mm) REVERT: E 143 TYR cc_start: 0.7980 (t80) cc_final: 0.7058 (m-80) REVERT: E 215 LYS cc_start: 0.7607 (mmtt) cc_final: 0.7067 (ptmm) REVERT: B 49 MET cc_start: 0.7001 (tmm) cc_final: 0.6493 (tmm) REVERT: B 142 ARG cc_start: 0.8104 (pmm-80) cc_final: 0.7121 (ptm160) REVERT: B 212 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7273 (p90) outliers start: 23 outliers final: 21 residues processed: 179 average time/residue: 0.0957 time to fit residues: 23.5839 Evaluate side-chains 186 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 54 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.109829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094863 restraints weight = 16735.288| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.56 r_work: 0.3281 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8809 Z= 0.116 Angle : 0.637 9.149 11995 Z= 0.314 Chirality : 0.044 0.177 1403 Planarity : 0.004 0.049 1483 Dihedral : 5.789 30.105 1595 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.91 % Allowed : 17.21 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.26), residues: 1036 helix: -1.22 (0.65), residues: 66 sheet: -0.88 (0.24), residues: 437 loop : -1.03 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.046 0.002 TYR D 72 PHE 0.009 0.001 PHE C 156 TRP 0.023 0.001 TRP D 123 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8783) covalent geometry : angle 0.62389 (11922) SS BOND : bond 0.00130 ( 5) SS BOND : angle 0.38639 ( 10) hydrogen bonds : bond 0.02486 ( 249) hydrogen bonds : angle 4.81741 ( 939) link_ALPHA1-2 : bond 0.00556 ( 1) link_ALPHA1-2 : angle 1.58472 ( 3) link_ALPHA1-3 : bond 0.00754 ( 3) link_ALPHA1-3 : angle 1.55187 ( 9) link_ALPHA1-6 : bond 0.00516 ( 1) link_ALPHA1-6 : angle 2.11535 ( 3) link_BETA1-4 : bond 0.00449 ( 10) link_BETA1-4 : angle 2.02479 ( 30) link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 1.80820 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.42 seconds wall clock time: 35 minutes 38.87 seconds (2138.87 seconds total)