Starting phenix.real_space_refine on Thu Feb 13 08:28:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dw1_8923/02_2025/6dw1_8923.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dw1_8923/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6dw1_8923/02_2025/6dw1_8923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dw1_8923/02_2025/6dw1_8923.map" model { file = "/net/cci-nas-00/data/ceres_data/6dw1_8923/02_2025/6dw1_8923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dw1_8923/02_2025/6dw1_8923.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} 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: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP: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: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS: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: {'GLU:plan': 1, 'ASP:plan': 3} 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: 6.10, per 1000 atoms: 0.71 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: 2.48 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.05 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: 2.37 Time building geometry restraints manager: 2.80 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 221 or resid 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 221 or resid 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: 12.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.210 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.370 Find NCS groups from input model: 0.340 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.180 ------------------------------------------------------------------------------- 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 8783 Z= 0.378 Angle : 0.972 13.768 11922 Z= 0.486 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP A 94 HIS 0.011 0.002 HIS A 101 PHE 0.026 0.003 PHE A 99 TYR 0.018 0.002 TYR C 168 ARG 0.011 0.001 ARG C 131 *********************** 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 : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8391 (mttt) cc_final: 0.8014 (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: 0.8544 (mt) REVERT: A 59 TYR cc_start: 0.9130 (p90) cc_final: 0.8882 (p90) REVERT: E 47 ILE cc_start: 0.9070 (mm) cc_final: 0.8677 (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: 0.2719 time to fit residues: 99.0420 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 : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 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 = 0.3648 r_free = 0.3648 target = 0.112340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097824 restraints weight = 16866.583| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.60 r_work: 0.3323 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8783 Z= 0.180 Angle : 0.719 8.782 11922 Z= 0.355 Chirality : 0.048 0.225 1403 Planarity : 0.005 0.057 1483 Dihedral : 16.688 100.354 1595 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.35 % Allowed : 11.51 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.24), residues: 1036 helix: -3.27 (0.41), residues: 62 sheet: -1.58 (0.23), residues: 423 loop : -2.02 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 94 HIS 0.007 0.001 HIS C 101 PHE 0.020 0.002 PHE C 64 TYR 0.014 0.001 TYR D 141 ARG 0.006 0.001 ARG B 114 *********************** 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 215 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8427 (mttt) cc_final: 0.7847 (tmtt) REVERT: C 75 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8050 (mmtp) REVERT: C 212 MET cc_start: 0.8458 (mmm) cc_final: 0.7727 (mmm) REVERT: A 17 ILE cc_start: 0.8943 (tp) cc_final: 0.8561 (tp) REVERT: A 39 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 59 TYR cc_start: 0.9177 (p90) cc_final: 0.8881 (p90) REVERT: E 47 ILE cc_start: 0.9151 (mm) cc_final: 0.8788 (mm) REVERT: E 103 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8138 (mtmm) REVERT: E 143 TYR cc_start: 0.8093 (t80) cc_final: 0.7114 (m-80) REVERT: B 49 MET cc_start: 0.6495 (tmm) cc_final: 0.6225 (mtt) REVERT: B 142 ARG cc_start: 0.7328 (pmm-80) cc_final: 0.6469 (ptm160) REVERT: B 160 THR cc_start: 0.8696 (m) cc_final: 0.8339 (p) outliers start: 21 outliers final: 9 residues processed: 208 average time/residue: 0.2116 time to fit residues: 59.9695 Evaluate side-chains 172 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.109522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094936 restraints weight = 17153.026| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.52 r_work: 0.3275 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8783 Z= 0.237 Angle : 0.695 8.407 11922 Z= 0.340 Chirality : 0.047 0.242 1403 Planarity : 0.005 0.053 1483 Dihedral : 12.166 92.411 1595 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.58 % Allowed : 11.84 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.25), residues: 1036 helix: -2.50 (0.53), residues: 64 sheet: -1.40 (0.24), residues: 436 loop : -1.65 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 94 HIS 0.005 0.001 HIS C 101 PHE 0.025 0.002 PHE C 64 TYR 0.015 0.002 TYR E 126 ARG 0.008 0.001 ARG C 172 *********************** 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 201 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8499 (mttt) cc_final: 0.7908 (tmtt) REVERT: C 212 MET cc_start: 0.8424 (mmm) cc_final: 0.7768 (mmm) REVERT: A 17 ILE cc_start: 0.8909 (tp) cc_final: 0.8625 (tp) REVERT: A 59 TYR cc_start: 0.9176 (p90) cc_final: 0.8857 (p90) REVERT: A 62 ASP cc_start: 0.7160 (p0) cc_final: 0.6883 (p0) REVERT: A 93 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8628 (pt) REVERT: E 47 ILE cc_start: 0.9168 (mm) cc_final: 0.8731 (mm) REVERT: E 103 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8134 (mtmm) REVERT: E 143 TYR cc_start: 0.8028 (t80) cc_final: 0.7041 (m-80) REVERT: B 49 MET cc_start: 0.6730 (tmm) cc_final: 0.6462 (mtt) REVERT: B 142 ARG cc_start: 0.7562 (pmm-80) cc_final: 0.6732 (ptm160) outliers start: 32 outliers final: 24 residues processed: 189 average time/residue: 0.2071 time to fit residues: 53.9306 Evaluate side-chains 180 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 130 MET 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 179 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 VAL 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 42 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN A 27 ASN A 195 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 = 0.3589 r_free = 0.3589 target = 0.108576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093746 restraints weight = 16872.929| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.56 r_work: 0.3256 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8783 Z= 0.235 Angle : 0.669 10.380 11922 Z= 0.326 Chirality : 0.047 0.260 1403 Planarity : 0.004 0.049 1483 Dihedral : 9.776 69.627 1595 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.36 % Allowed : 11.06 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.25), residues: 1036 helix: -1.99 (0.60), residues: 64 sheet: -1.28 (0.23), residues: 455 loop : -1.51 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.005 0.001 HIS C 101 PHE 0.015 0.002 PHE C 64 TYR 0.015 0.001 TYR E 126 ARG 0.004 0.000 ARG C 172 *********************** 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 203 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7677 (t0) REVERT: D 98 LEU cc_start: 0.8978 (mm) cc_final: 0.8769 (mt) REVERT: D 214 LYS cc_start: 0.8542 (mttt) cc_final: 0.7897 (tmtt) REVERT: C 212 MET cc_start: 0.8395 (mmm) cc_final: 0.7773 (mmm) REVERT: A 27 ASN cc_start: 0.8325 (t0) cc_final: 0.8068 (t0) REVERT: A 62 ASP cc_start: 0.7170 (p0) cc_final: 0.6926 (p0) REVERT: E 47 ILE cc_start: 0.9143 (mm) cc_final: 0.8752 (mm) REVERT: E 143 TYR cc_start: 0.8041 (t80) cc_final: 0.7049 (m-80) REVERT: B 49 MET cc_start: 0.6809 (tmm) cc_final: 0.6424 (mtt) REVERT: B 142 ARG cc_start: 0.7728 (pmm-80) cc_final: 0.6821 (ptm160) outliers start: 39 outliers final: 31 residues processed: 186 average time/residue: 0.2092 time to fit residues: 54.0667 Evaluate side-chains 186 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 100 SER 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 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 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 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 165 GLU 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 160 THR Chi-restraints excluded: chain B residue 176 THR 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 29 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 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 = 0.3600 r_free = 0.3600 target = 0.109480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094618 restraints weight = 16813.636| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.56 r_work: 0.3270 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8783 Z= 0.190 Angle : 0.645 12.954 11922 Z= 0.314 Chirality : 0.045 0.262 1403 Planarity : 0.004 0.049 1483 Dihedral : 8.783 64.770 1595 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.69 % Allowed : 12.74 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.26), residues: 1036 helix: -1.73 (0.62), residues: 64 sheet: -1.17 (0.23), residues: 452 loop : -1.44 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 123 HIS 0.004 0.001 HIS C 101 PHE 0.011 0.001 PHE C 64 TYR 0.020 0.001 TYR E 11 ARG 0.004 0.000 ARG C 172 *********************** 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 198 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7682 (t0) REVERT: D 214 LYS cc_start: 0.8520 (mttt) cc_final: 0.7873 (tmtt) REVERT: C 75 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7976 (mmtp) REVERT: C 212 MET cc_start: 0.8363 (mmm) cc_final: 0.7743 (mmm) REVERT: A 27 ASN cc_start: 0.8309 (t0) cc_final: 0.8095 (m-40) REVERT: E 47 ILE cc_start: 0.9132 (mm) cc_final: 0.8812 (mm) REVERT: E 103 LYS cc_start: 0.8400 (mtmm) cc_final: 0.8138 (mtmm) REVERT: E 143 TYR cc_start: 0.8019 (t80) cc_final: 0.7084 (m-80) REVERT: B 49 MET cc_start: 0.6832 (tmm) cc_final: 0.6541 (tmm) REVERT: B 90 GLN cc_start: 0.8394 (mm110) cc_final: 0.8110 (mm-40) REVERT: B 142 ARG cc_start: 0.7765 (pmm-80) cc_final: 0.6858 (ptm160) outliers start: 33 outliers final: 26 residues processed: 185 average time/residue: 0.2093 time to fit residues: 52.9422 Evaluate side-chains 184 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 100 SER 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 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 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 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR 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 182 GLU 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 64 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN A 195 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 = 0.3570 r_free = 0.3570 target = 0.107626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.092377 restraints weight = 16776.211| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.55 r_work: 0.3234 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8783 Z= 0.282 Angle : 0.665 10.709 11922 Z= 0.328 Chirality : 0.046 0.265 1403 Planarity : 0.004 0.051 1483 Dihedral : 8.241 59.774 1595 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.25 % Allowed : 13.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.26), residues: 1036 helix: -1.58 (0.63), residues: 64 sheet: -1.12 (0.23), residues: 445 loop : -1.33 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 123 HIS 0.005 0.001 HIS D 122 PHE 0.012 0.002 PHE E 212 TYR 0.015 0.002 TYR E 126 ARG 0.004 0.000 ARG B 41 *********************** 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 198 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7669 (t0) REVERT: D 214 LYS cc_start: 0.8540 (mttt) cc_final: 0.7944 (tmtt) REVERT: C 212 MET cc_start: 0.8359 (mmm) cc_final: 0.7787 (mmm) REVERT: A 89 MET cc_start: 0.8890 (tpt) cc_final: 0.8583 (tpp) REVERT: E 47 ILE cc_start: 0.9139 (mm) cc_final: 0.8814 (mm) REVERT: E 103 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8177 (mtmm) REVERT: E 143 TYR cc_start: 0.8092 (t80) cc_final: 0.7110 (m-80) REVERT: B 49 MET cc_start: 0.6948 (tmm) cc_final: 0.6595 (tmm) REVERT: B 142 ARG cc_start: 0.7882 (pmm-80) cc_final: 0.6951 (ptm160) outliers start: 38 outliers final: 33 residues processed: 184 average time/residue: 0.1978 time to fit residues: 50.7368 Evaluate side-chains 187 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 100 SER 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 107 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 99 LEU Chi-restraints excluded: chain E residue 160 THR 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 176 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 58 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 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 = 0.3557 r_free = 0.3557 target = 0.107134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.092086 restraints weight = 16982.079| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.57 r_work: 0.3222 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8783 Z= 0.289 Angle : 0.670 10.581 11922 Z= 0.333 Chirality : 0.046 0.261 1403 Planarity : 0.004 0.052 1483 Dihedral : 7.844 55.084 1595 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.25 % Allowed : 13.85 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.25), residues: 1036 helix: -1.49 (0.63), residues: 64 sheet: -1.12 (0.23), residues: 445 loop : -1.33 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 123 HIS 0.004 0.001 HIS D 122 PHE 0.011 0.002 PHE E 212 TYR 0.016 0.002 TYR A 59 ARG 0.003 0.000 ARG B 41 *********************** 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 196 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7694 (t0) REVERT: D 197 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5945 (ptt180) REVERT: D 214 LYS cc_start: 0.8574 (mttt) cc_final: 0.7962 (tmtt) REVERT: C 212 MET cc_start: 0.8346 (mmm) cc_final: 0.7804 (mmm) REVERT: E 47 ILE cc_start: 0.9127 (mm) cc_final: 0.8806 (mm) REVERT: E 103 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8200 (mtmm) REVERT: E 143 TYR cc_start: 0.8091 (t80) cc_final: 0.7103 (m-80) REVERT: B 49 MET cc_start: 0.7018 (tmm) cc_final: 0.6623 (tmm) REVERT: B 142 ARG cc_start: 0.7997 (pmm-80) cc_final: 0.7002 (ptm160) REVERT: B 160 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8658 (p) outliers start: 38 outliers final: 31 residues processed: 182 average time/residue: 0.2027 time to fit residues: 51.1077 Evaluate side-chains 186 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 100 SER 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 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 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR 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 160 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 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 = 0.3590 r_free = 0.3590 target = 0.108864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093625 restraints weight = 17006.934| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.58 r_work: 0.3255 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8783 Z= 0.191 Angle : 0.636 10.622 11922 Z= 0.315 Chirality : 0.044 0.242 1403 Planarity : 0.004 0.049 1483 Dihedral : 7.227 50.089 1595 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.58 % Allowed : 14.86 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.26), residues: 1036 helix: -1.29 (0.65), residues: 64 sheet: -1.08 (0.23), residues: 446 loop : -1.25 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 123 HIS 0.004 0.001 HIS A 150 PHE 0.009 0.001 PHE C 64 TYR 0.016 0.001 TYR A 59 ARG 0.003 0.000 ARG B 41 *********************** 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 194 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7599 (t0) REVERT: D 214 LYS cc_start: 0.8498 (mttt) cc_final: 0.7895 (tmtt) REVERT: C 212 MET cc_start: 0.8324 (mmm) cc_final: 0.7719 (mmm) REVERT: E 47 ILE cc_start: 0.9107 (mm) cc_final: 0.8711 (mm) REVERT: E 103 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8170 (mtmm) REVERT: E 143 TYR cc_start: 0.8036 (t80) cc_final: 0.7074 (m-80) REVERT: B 49 MET cc_start: 0.6945 (tmm) cc_final: 0.6514 (tmm) REVERT: B 90 GLN cc_start: 0.8378 (mm110) cc_final: 0.8112 (mm-40) REVERT: B 142 ARG cc_start: 0.8002 (pmm-80) cc_final: 0.7008 (ptm160) REVERT: B 160 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8557 (p) outliers start: 32 outliers final: 26 residues processed: 179 average time/residue: 0.2056 time to fit residues: 50.8300 Evaluate side-chains 189 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 100 SER 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 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 A residue 47 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 67 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095251 restraints weight = 16848.340| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.57 r_work: 0.3278 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8783 Z= 0.162 Angle : 0.619 10.593 11922 Z= 0.307 Chirality : 0.044 0.220 1403 Planarity : 0.004 0.048 1483 Dihedral : 6.624 43.667 1595 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.46 % Allowed : 15.53 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.26), residues: 1036 helix: -1.30 (0.65), residues: 66 sheet: -1.02 (0.24), residues: 430 loop : -1.21 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 123 HIS 0.003 0.001 HIS D 122 PHE 0.009 0.001 PHE C 64 TYR 0.015 0.001 TYR A 59 ARG 0.003 0.000 ARG B 41 *********************** 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 202 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7465 (t0) REVERT: D 214 LYS cc_start: 0.8470 (mttt) cc_final: 0.7884 (tmtt) REVERT: C 212 MET cc_start: 0.8328 (mmm) cc_final: 0.7712 (mmm) REVERT: A 89 MET cc_start: 0.8811 (tpt) cc_final: 0.8533 (tpp) REVERT: E 47 ILE cc_start: 0.9097 (mm) cc_final: 0.8685 (mm) REVERT: E 103 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8167 (mtmm) REVERT: E 143 TYR cc_start: 0.8012 (t80) cc_final: 0.7083 (m-80) REVERT: B 49 MET cc_start: 0.6931 (tmm) cc_final: 0.6509 (tmm) REVERT: B 90 GLN cc_start: 0.8390 (mm110) cc_final: 0.8131 (mm-40) REVERT: B 142 ARG cc_start: 0.7949 (pmm-80) cc_final: 0.6948 (ptm160) REVERT: B 160 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8507 (p) outliers start: 31 outliers final: 24 residues processed: 188 average time/residue: 0.2093 time to fit residues: 53.5315 Evaluate side-chains 184 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 100 SER 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 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 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 A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 0.0050 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** 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 = 0.3621 r_free = 0.3621 target = 0.110799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095681 restraints weight = 16656.633| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.56 r_work: 0.3289 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8783 Z= 0.166 Angle : 0.621 10.432 11922 Z= 0.309 Chirality : 0.044 0.194 1403 Planarity : 0.004 0.048 1483 Dihedral : 6.221 37.947 1595 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.24 % Allowed : 15.75 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.26), residues: 1036 helix: -1.25 (0.66), residues: 66 sheet: -0.87 (0.24), residues: 417 loop : -1.13 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 123 HIS 0.004 0.001 HIS D 122 PHE 0.009 0.001 PHE C 64 TYR 0.020 0.001 TYR E 11 ARG 0.005 0.000 ARG B 216 ********************** 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 192 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7379 (t0) REVERT: D 214 LYS cc_start: 0.8456 (mttt) cc_final: 0.7884 (tmtt) REVERT: C 212 MET cc_start: 0.8341 (mmm) cc_final: 0.7725 (mmm) REVERT: A 59 TYR cc_start: 0.9082 (p90) cc_final: 0.8489 (p90) REVERT: A 89 MET cc_start: 0.8796 (tpt) cc_final: 0.8515 (tpp) REVERT: E 47 ILE cc_start: 0.9098 (mm) cc_final: 0.8675 (mm) REVERT: E 103 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8133 (mtmm) REVERT: E 143 TYR cc_start: 0.7983 (t80) cc_final: 0.7091 (m-80) REVERT: B 49 MET cc_start: 0.6827 (tmm) cc_final: 0.6431 (tmm) REVERT: B 90 GLN cc_start: 0.8381 (mm110) cc_final: 0.8129 (mm-40) REVERT: B 142 ARG cc_start: 0.7703 (pmm-80) cc_final: 0.6814 (ptm160) REVERT: B 160 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8485 (p) REVERT: B 185 GLN cc_start: 0.7558 (pt0) cc_final: 0.7064 (tt0) outliers start: 29 outliers final: 26 residues processed: 181 average time/residue: 0.2004 time to fit residues: 51.2023 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 : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 100 SER 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 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 33 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR 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 176 THR Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** A 27 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.107848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093077 restraints weight = 16930.107| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.53 r_work: 0.3241 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8783 Z= 0.287 Angle : 0.662 10.619 11922 Z= 0.332 Chirality : 0.046 0.193 1403 Planarity : 0.004 0.052 1483 Dihedral : 6.284 35.136 1595 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.46 % Allowed : 15.87 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.26), residues: 1036 helix: -1.32 (0.65), residues: 66 sheet: -0.94 (0.23), residues: 440 loop : -1.21 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 123 HIS 0.005 0.001 HIS D 122 PHE 0.010 0.002 PHE E 212 TYR 0.016 0.002 TYR A 59 ARG 0.003 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3954.98 seconds wall clock time: 71 minutes 31.82 seconds (4291.82 seconds total)