Starting phenix.real_space_refine on Thu Mar 13 10:39:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dw1_8923/03_2025/6dw1_8923.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dw1_8923/03_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_8923/03_2025/6dw1_8923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dw1_8923/03_2025/6dw1_8923.map" model { file = "/net/cci-nas-00/data/ceres_data/6dw1_8923/03_2025/6dw1_8923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dw1_8923/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.35, per 1000 atoms: 0.86 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: 2.83 Conformation dependent library (CDL) restraints added in 933.4 milliseconds 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: 1.20 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: 2.32 Time building geometry restraints manager: 3.16 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: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.250 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- 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 : 0.953 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: 0.2659 time to fit residues: 96.6473 Evaluate side-chains 172 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097818 restraints weight = 16866.583| |-----------------------------------------------------------------------------| r_work (start): 0.3426 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 : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8426 (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: 0.7583 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 59 TYR cc_start: 0.9176 (p90) cc_final: 0.8880 (p90) REVERT: E 47 ILE cc_start: 0.9150 (mm) cc_final: 0.8788 (mm) REVERT: E 103 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8137 (mtmm) REVERT: E 143 TYR cc_start: 0.8093 (t80) cc_final: 0.7113 (m-80) REVERT: B 49 MET cc_start: 0.6494 (tmm) cc_final: 0.6222 (mtt) REVERT: B 142 ARG cc_start: 0.7326 (pmm-80) cc_final: 0.6470 (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: 0.2080 time to fit residues: 59.1828 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 : 0.936 ------------------------------------------------------------------------------- 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: 0.0060 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 63 optimal weight: 3.9990 overall best weight: 1.2118 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.109821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095278 restraints weight = 17143.827| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.51 r_work: 0.3282 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8783 Z= 0.226 Angle : 0.689 8.333 11922 Z= 0.337 Chirality : 0.047 0.241 1403 Planarity : 0.004 0.052 1483 Dihedral : 12.166 92.221 1595 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.35 % Allowed : 11.96 % Favored : 84.69 % 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: -2.48 (0.25), residues: 1036 helix: -2.54 (0.52), residues: 64 sheet: -1.40 (0.24), residues: 434 loop : -1.67 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.005 0.001 HIS C 101 PHE 0.025 0.002 PHE C 64 TYR 0.014 0.002 TYR E 126 ARG 0.008 0.000 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 198 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8489 (mttt) cc_final: 0.7902 (tmtt) REVERT: C 212 MET cc_start: 0.8423 (mmm) cc_final: 0.7770 (mmm) REVERT: A 17 ILE cc_start: 0.8909 (tp) cc_final: 0.8632 (tp) REVERT: A 27 ASN cc_start: 0.8265 (t0) cc_final: 0.7936 (t0) REVERT: A 59 TYR cc_start: 0.9178 (p90) cc_final: 0.8866 (p90) REVERT: A 62 ASP cc_start: 0.7171 (p0) cc_final: 0.6884 (p0) REVERT: A 93 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (pt) REVERT: E 47 ILE cc_start: 0.9165 (mm) cc_final: 0.8728 (mm) REVERT: E 103 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8146 (mtmm) REVERT: E 143 TYR cc_start: 0.8015 (t80) cc_final: 0.7041 (m-80) REVERT: B 49 MET cc_start: 0.6692 (tmm) cc_final: 0.6393 (mtt) REVERT: B 142 ARG cc_start: 0.7525 (pmm-80) cc_final: 0.6676 (ptm160) outliers start: 30 outliers final: 25 residues processed: 187 average time/residue: 0.2033 time to fit residues: 52.5307 Evaluate side-chains 180 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 167 VAL 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: 0.0170 chunk 77 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.109887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095131 restraints weight = 16842.268| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.56 r_work: 0.3281 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8783 Z= 0.200 Angle : 0.660 10.058 11922 Z= 0.321 Chirality : 0.046 0.258 1403 Planarity : 0.004 0.048 1483 Dihedral : 9.905 70.174 1595 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.13 % Allowed : 10.84 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.25 (0.25), residues: 1036 helix: -1.98 (0.60), residues: 64 sheet: -1.27 (0.24), residues: 432 loop : -1.55 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.004 0.001 HIS C 101 PHE 0.014 0.001 PHE C 64 TYR 0.014 0.001 TYR E 126 ARG 0.005 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 206 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8951 (mm) cc_final: 0.8719 (mt) REVERT: D 214 LYS cc_start: 0.8487 (mttt) cc_final: 0.7864 (tmtt) REVERT: C 106 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8743 (p) REVERT: C 212 MET cc_start: 0.8420 (mmm) cc_final: 0.7770 (mmm) REVERT: A 27 ASN cc_start: 0.8300 (t0) cc_final: 0.7941 (t0) REVERT: E 47 ILE cc_start: 0.9146 (mm) cc_final: 0.8845 (mm) REVERT: E 143 TYR cc_start: 0.8022 (t80) cc_final: 0.7026 (m-80) REVERT: B 49 MET cc_start: 0.6749 (tmm) cc_final: 0.6508 (tmm) REVERT: B 142 ARG cc_start: 0.7662 (pmm-80) cc_final: 0.6774 (ptm160) outliers start: 37 outliers final: 28 residues processed: 191 average time/residue: 0.2045 time to fit residues: 53.9654 Evaluate side-chains 185 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 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 188 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2624 > 50: distance: 33 - 37: 14.809 distance: 37 - 38: 23.240 distance: 38 - 39: 9.504 distance: 38 - 41: 19.819 distance: 39 - 40: 25.645 distance: 39 - 45: 26.884 distance: 41 - 42: 25.052 distance: 42 - 43: 7.360 distance: 43 - 44: 10.783 distance: 45 - 46: 21.539 distance: 46 - 47: 30.215 distance: 46 - 49: 32.377 distance: 47 - 48: 27.641 distance: 47 - 53: 37.799 distance: 49 - 50: 32.968 distance: 50 - 51: 39.902 distance: 51 - 52: 37.803 distance: 53 - 54: 13.292 distance: 54 - 55: 23.473 distance: 54 - 57: 42.094 distance: 55 - 56: 28.242 distance: 55 - 58: 17.421 distance: 58 - 59: 9.817 distance: 59 - 60: 3.289 distance: 59 - 62: 61.104 distance: 60 - 61: 60.335 distance: 60 - 66: 41.833 distance: 62 - 63: 46.098 distance: 63 - 64: 25.335 distance: 63 - 65: 58.040 distance: 66 - 67: 42.378 distance: 67 - 68: 41.785 distance: 67 - 70: 38.817 distance: 68 - 69: 50.312 distance: 68 - 77: 28.052 distance: 70 - 71: 58.105 distance: 71 - 72: 43.137 distance: 72 - 73: 10.347 distance: 73 - 74: 14.188 distance: 74 - 75: 14.212 distance: 74 - 76: 18.971 distance: 77 - 78: 40.999 distance: 78 - 79: 27.438 distance: 78 - 81: 29.416 distance: 79 - 80: 43.657 distance: 79 - 88: 6.074 distance: 81 - 82: 10.640 distance: 82 - 83: 30.042 distance: 83 - 84: 5.148 distance: 84 - 85: 4.969 distance: 85 - 86: 6.391 distance: 85 - 87: 9.375 distance: 88 - 89: 10.259 distance: 89 - 90: 20.801 distance: 89 - 92: 33.153 distance: 90 - 91: 33.305 distance: 90 - 100: 11.942 distance: 92 - 93: 16.615 distance: 93 - 94: 14.250 distance: 93 - 95: 10.022 distance: 94 - 96: 24.913 distance: 95 - 97: 12.519 distance: 96 - 98: 5.663 distance: 97 - 98: 12.924 distance: 98 - 99: 10.908 distance: 100 - 101: 18.252 distance: 100 - 106: 15.445 distance: 101 - 102: 42.245 distance: 101 - 104: 37.539 distance: 102 - 103: 23.979 distance: 102 - 107: 31.495 distance: 104 - 105: 39.439 distance: 105 - 106: 23.118 distance: 107 - 108: 24.106 distance: 108 - 109: 39.814 distance: 108 - 111: 38.735 distance: 109 - 110: 26.272 distance: 111 - 112: 29.703 distance: 112 - 113: 51.894 distance: 112 - 114: 32.696 distance: 115 - 116: 9.999 distance: 116 - 117: 18.347 distance: 116 - 119: 13.294 distance: 117 - 118: 15.178 distance: 117 - 123: 21.211 distance: 119 - 120: 26.915 distance: 120 - 121: 15.865 distance: 120 - 122: 36.323