Starting phenix.real_space_refine on Sat Feb 7 13:49:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uk1_8563/02_2026/5uk1_8563_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uk1_8563/02_2026/5uk1_8563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5uk1_8563/02_2026/5uk1_8563_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uk1_8563/02_2026/5uk1_8563_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5uk1_8563/02_2026/5uk1_8563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uk1_8563/02_2026/5uk1_8563.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.069 sd= 0.375 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 11004 2.51 5 N 2985 2.21 5 O 3483 1.98 5 H 16401 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33948 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "E" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "F" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "G" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 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: "L" 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: "M" 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: "N" 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: "O" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.24, per 1000 atoms: 0.18 Number of scatterers: 33948 At special positions: 0 Unit cell: (141.04, 129.56, 182.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3483 8.00 N 2985 7.00 C 11004 6.00 H 16401 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 637 " distance=2.05 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=1.96 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 644 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=2.06 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.04 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.04 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 BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 406 " - " ASN A 129 " " NAG A 407 " - " ASN A 163 " " NAG A 408 " - " ASN A 15 " " NAG A 409 " - " ASN A 27 " " NAG A 410 " - " ASN A 290 " " NAG B 701 " - " ASN B 654 " " NAG C 406 " - " ASN C 129 " " NAG C 407 " - " ASN C 163 " " NAG C 408 " - " ASN C 15 " " NAG C 409 " - " ASN C 27 " " NAG C 410 " - " ASN C 290 " " NAG D 701 " - " ASN D 654 " " NAG E 406 " - " ASN E 129 " " NAG E 407 " - " ASN E 163 " " NAG E 408 " - " ASN E 15 " " NAG E 409 " - " ASN E 27 " " NAG E 410 " - " ASN E 290 " " NAG F 701 " - " ASN F 654 " " NAG J 1 " - " ASN A 91 " " NAG K 1 " - " ASN A 58 " " NAG L 1 " - " ASN C 91 " " NAG M 1 " - " ASN C 58 " " NAG N 1 " - " ASN E 91 " " NAG O 1 " - " ASN E 58 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 48 sheets defined 18.4% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.083A pdb=" N GLY A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.166A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.994A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 557 Processing helix chain 'B' and resid 574 through 626 removed outlier: 3.803A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 654 Processing helix chain 'B' and resid 662 through 670 Processing helix chain 'C' and resid 60 through 67 removed outlier: 4.084A pdb=" N GLY C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.166A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.995A pdb=" N GLN C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 557 Processing helix chain 'D' and resid 574 through 626 removed outlier: 3.802A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'E' and resid 60 through 67 removed outlier: 4.084A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.166A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.994A pdb=" N GLN E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 557 Processing helix chain 'F' and resid 574 through 626 removed outlier: 3.803A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 654 Processing helix chain 'F' and resid 662 through 670 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.535A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 215 Processing sheet with id=AA1, first strand: chain 'B' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 48 removed outlier: 5.917A pdb=" N LEU A 47 " --> pdb=" O ALA A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB6, first strand: chain 'C' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU C 47 " --> pdb=" O ALA C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AC7, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'E' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU E 47 " --> pdb=" O ALA E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.602A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD2, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.707A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 287 through 289 removed outlier: 3.922A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AE1, first strand: chain 'G' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY G 141 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE6, first strand: chain 'H' and resid 129 through 132 removed outlier: 5.810A pdb=" N GLY H 141 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 136 through 137 removed outlier: 6.992A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AF2, first strand: chain 'I' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY I 141 " --> pdb=" O ASN I 209 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1845 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: 9.63 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 16395 1.01 - 1.21: 6 1.21 - 1.42: 7627 1.42 - 1.62: 10214 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA TRP I 36 " pdb=" CB TRP I 36 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.82e-02 3.02e+03 7.03e+00 bond pdb=" CA TRP H 36 " pdb=" CB TRP H 36 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.82e-02 3.02e+03 6.87e+00 bond pdb=" CA TRP G 36 " pdb=" CB TRP G 36 " ideal model delta sigma weight residual 1.532 1.484 0.047 1.82e-02 3.02e+03 6.80e+00 bond pdb=" NE1 TRP C 153 " pdb=" HE1 TRP C 153 " ideal model delta sigma weight residual 0.860 0.809 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" NE1 TRP A 153 " pdb=" HE1 TRP A 153 " ideal model delta sigma weight residual 0.860 0.810 0.050 2.00e-02 2.50e+03 6.34e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 55733 2.10 - 4.20: 5029 4.20 - 6.30: 665 6.30 - 8.40: 108 8.40 - 10.51: 22 Bond angle restraints: 61557 Sorted by residual: angle pdb=" C GLU I 1 " pdb=" N ILE I 2 " pdb=" CA ILE I 2 " ideal model delta sigma weight residual 120.35 127.76 -7.41 1.39e+00 5.18e-01 2.84e+01 angle pdb=" C GLU G 1 " pdb=" N ILE G 2 " pdb=" CA ILE G 2 " ideal model delta sigma weight residual 120.35 127.73 -7.38 1.39e+00 5.18e-01 2.82e+01 angle pdb=" C GLU H 1 " pdb=" N ILE H 2 " pdb=" CA ILE H 2 " ideal model delta sigma weight residual 120.35 127.69 -7.34 1.39e+00 5.18e-01 2.79e+01 angle pdb=" N SER H 30 " pdb=" CA SER H 30 " pdb=" C SER H 30 " ideal model delta sigma weight residual 113.28 121.54 -8.26 1.57e+00 4.06e-01 2.77e+01 angle pdb=" N SER I 30 " pdb=" CA SER I 30 " pdb=" C SER I 30 " ideal model delta sigma weight residual 113.28 121.53 -8.25 1.57e+00 4.06e-01 2.76e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 15607 19.35 - 38.71: 867 38.71 - 58.06: 271 58.06 - 77.42: 46 77.42 - 96.77: 15 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA GLY I 58 " pdb=" C GLY I 58 " pdb=" N ILE I 59 " pdb=" CA ILE I 59 " ideal model delta harmonic sigma weight residual -180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA GLY H 58 " pdb=" C GLY H 58 " pdb=" N ILE H 59 " pdb=" CA ILE H 59 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA GLY G 58 " pdb=" C GLY G 58 " pdb=" N ILE G 59 " pdb=" CA ILE G 59 " ideal model delta harmonic sigma weight residual -180.00 -147.51 -32.49 0 5.00e+00 4.00e-02 4.22e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2235 0.081 - 0.163: 398 0.163 - 0.244: 43 0.244 - 0.326: 11 0.326 - 0.407: 7 Chirality restraints: 2694 Sorted by residual: chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.76e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.66e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.53e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 248 " -0.149 2.00e-02 2.50e+03 1.75e-01 4.60e+02 pdb=" CG ASN E 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN E 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN E 248 " 0.260 2.00e-02 2.50e+03 pdb="HD22 ASN E 248 " -0.263 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 248 " -0.148 2.00e-02 2.50e+03 1.74e-01 4.56e+02 pdb=" CG ASN A 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN A 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 248 " 0.259 2.00e-02 2.50e+03 pdb="HD22 ASN A 248 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 248 " 0.148 2.00e-02 2.50e+03 1.74e-01 4.53e+02 pdb=" CG ASN C 248 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 248 " -0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN C 248 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 248 " -0.258 2.00e-02 2.50e+03 pdb="HD22 ASN C 248 " 0.261 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 7614 2.31 - 2.88: 77229 2.88 - 3.45: 86327 3.45 - 4.03: 119135 4.03 - 4.60: 178874 Nonbonded interactions: 469179 Sorted by model distance: nonbonded pdb=" H GLY H 140 " pdb=" O LEU H 210 " model vdw 1.735 2.450 nonbonded pdb=" H THR E 31 " pdb=" O LEU E 321 " model vdw 1.736 2.450 nonbonded pdb=" H THR C 31 " pdb=" O LEU C 321 " model vdw 1.736 2.450 nonbonded pdb=" H THR A 31 " pdb=" O LEU A 321 " model vdw 1.737 2.450 nonbonded pdb=" H GLY G 140 " pdb=" O LEU G 210 " model vdw 1.738 2.450 ... (remaining 469174 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.200 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.720 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.010 0.083 17997 Z= 0.467 Angle : 1.305 9.783 24459 Z= 0.751 Chirality : 0.065 0.407 2694 Planarity : 0.009 0.082 3132 Dihedral : 12.045 96.773 7023 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.06 % Favored : 91.80 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.14), residues: 2172 helix: -1.38 (0.22), residues: 348 sheet: -2.97 (0.17), residues: 546 loop : -2.94 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG H 222 TYR 0.032 0.005 TYR C 95 PHE 0.036 0.004 PHE D 509 TRP 0.029 0.005 TRP A 127 HIS 0.019 0.005 HIS D 611 Details of bonding type rmsd covalent geometry : bond 0.01011 (17943) covalent geometry : angle 1.28106 (24318) SS BOND : bond 0.01864 ( 21) SS BOND : angle 2.19512 ( 42) hydrogen bonds : bond 0.10955 ( 654) hydrogen bonds : angle 11.13390 ( 1845) link_BETA1-4 : bond 0.01125 ( 9) link_BETA1-4 : angle 4.08142 ( 27) link_NAG-ASN : bond 0.01180 ( 24) link_NAG-ASN : angle 3.93090 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8881 (t0) cc_final: 0.8657 (t0) REVERT: A 83 ILE cc_start: 0.9525 (mt) cc_final: 0.9037 (mt) REVERT: A 84 VAL cc_start: 0.8884 (t) cc_final: 0.8370 (t) REVERT: A 184 HIS cc_start: 0.8971 (m90) cc_final: 0.8444 (m-70) REVERT: A 212 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7656 (mmtm) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1727 time to fit residues: 13.7837 Evaluate side-chains 52 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.140 Evaluate side-chains 78 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9504 (tp40) cc_final: 0.9099 (tp-100) REVERT: B 576 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8188 (ttt180) REVERT: B 588 PHE cc_start: 0.8947 (m-80) cc_final: 0.8646 (m-80) REVERT: B 598 LEU cc_start: 0.9568 (mt) cc_final: 0.9019 (mt) REVERT: B 619 TYR cc_start: 0.7929 (t80) cc_final: 0.7710 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1846 time to fit residues: 15.3189 Evaluate side-chains 45 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.045 Evaluate side-chains 55 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 LEU cc_start: 0.9468 (tp) cc_final: 0.9063 (pp) REVERT: G 204 TYR cc_start: 0.8539 (m-80) cc_final: 0.7956 (m-80) REVERT: G 219 PHE cc_start: 0.8743 (m-80) cc_final: 0.7782 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2366 time to fit residues: 13.9308 Evaluate side-chains 33 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.086 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044252 restraints weight = 43140.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047268 restraints weight = 21526.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049576 restraints weight = 12722.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051289 restraints weight = 8174.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052530 restraints weight = 5558.299| |-----------------------------------------------------------------------------| r_work (final): 0.3250 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056829 restraints weight = 22042.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060148 restraints weight = 12377.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062672 restraints weight = 7847.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064534 restraints weight = 5325.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.065903 restraints weight = 3758.329| |-----------------------------------------------------------------------------| r_work (final): 0.3631 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.062919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.048985 restraints weight = 36679.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.052627 restraints weight = 20226.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.055366 restraints weight = 12469.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.057359 restraints weight = 8175.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.058773 restraints weight = 5529.227| |-----------------------------------------------------------------------------| r_work (final): 0.3609 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.038018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.035737 restraints weight = 663.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.036111 restraints weight = 388.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.036412 restraints weight = 277.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.036613 restraints weight = 214.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.036761 restraints weight = 174.934| |-----------------------------------------------------------------------------| r_work (final): 0.2366 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.054931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054479 restraints weight = 463.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054772 restraints weight = 109.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054867 restraints weight = 33.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054912 restraints weight = 12.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054906 restraints weight = 4.178 | |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 17997 Z= 0.251 Angle : 0.927 12.804 24459 Z= 0.496 Chirality : 0.048 0.226 2694 Planarity : 0.015 0.403 3132 Dihedral : 11.240 70.491 3075 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.32 % Allowed : 2.27 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.14), residues: 2172 helix: -0.75 (0.26), residues: 336 sheet: -2.75 (0.18), residues: 507 loop : -2.88 (0.13), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG F 575 TYR 0.025 0.002 TYR A 102 PHE 0.022 0.002 PHE B 509 TRP 0.015 0.002 TRP C 127 HIS 0.017 0.002 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00536 (17943) covalent geometry : angle 0.90049 (24318) SS BOND : bond 0.01888 ( 21) SS BOND : angle 1.38874 ( 42) hydrogen bonds : bond 0.08505 ( 654) hydrogen bonds : angle 8.63627 ( 1845) link_BETA1-4 : bond 0.01496 ( 9) link_BETA1-4 : angle 4.95647 ( 27) link_NAG-ASN : bond 0.00790 ( 24) link_NAG-ASN : angle 2.79130 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ASP cc_start: 0.9313 (t0) cc_final: 0.8995 (t0) REVERT: C 204 VAL cc_start: 0.9515 (m) cc_final: 0.9296 (m) REVERT: C 209 TYR cc_start: 0.9412 (t80) cc_final: 0.9182 (t80) REVERT: C 231 ASN cc_start: 0.9676 (m-40) cc_final: 0.9366 (t0) outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.0840 time to fit residues: 6.3398 Evaluate side-chains 43 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.135 Evaluate side-chains 59 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9748 (tp40) cc_final: 0.9447 (tp-100) REVERT: B 576 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8380 (ttt180) REVERT: B 602 LEU cc_start: 0.9650 (tt) cc_final: 0.9436 (tp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1260 time to fit residues: 8.1706 Evaluate side-chains 44 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.074 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 204 TYR cc_start: 0.8762 (m-80) cc_final: 0.8078 (m-80) REVERT: H 218 TYR cc_start: 0.9037 (m-10) cc_final: 0.8738 (m-10) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.3047 time to fit residues: 12.5753 Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.089 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.0296 > 50: distance: 1 - 2: 20.679 distance: 1 - 9: 29.385 distance: 2 - 3: 32.307 distance: 2 - 5: 23.943 distance: 2 - 10: 22.336 distance: 3 - 4: 13.178 distance: 3 - 20: 31.494 distance: 5 - 6: 7.578 distance: 5 - 7: 22.129 distance: 5 - 11: 4.745 distance: 6 - 8: 8.137 distance: 6 - 12: 4.668 distance: 6 - 13: 3.277 distance: 7 - 14: 8.807 distance: 7 - 15: 11.000 distance: 7 - 16: 19.382 distance: 8 - 18: 3.132 distance: 8 - 19: 3.350 distance: 20 - 21: 27.152 distance: 20 - 28: 19.013 distance: 21 - 22: 51.949 distance: 21 - 24: 21.211 distance: 21 - 29: 19.508 distance: 22 - 23: 32.166 distance: 22 - 39: 30.461 distance: 24 - 25: 26.131 distance: 24 - 30: 25.079 distance: 24 - 31: 28.079 distance: 25 - 26: 10.184 distance: 25 - 27: 12.118 distance: 25 - 32: 6.657 distance: 26 - 33: 5.868 distance: 26 - 34: 4.261 distance: 26 - 35: 4.675 distance: 27 - 36: 9.150 distance: 27 - 37: 13.182 distance: 27 - 38: 9.169 distance: 39 - 40: 30.682 distance: 39 - 43: 30.062 distance: 40 - 41: 48.680 distance: 40 - 44: 29.897 distance: 40 - 45: 40.458 distance: 41 - 42: 38.074 distance: 41 - 46: 40.497 distance: 46 - 47: 55.320 distance: 46 - 54: 30.878 distance: 47 - 48: 55.430 distance: 47 - 50: 22.459 distance: 47 - 55: 31.772 distance: 48 - 49: 52.660 distance: 48 - 60: 68.030 distance: 50 - 51: 58.383 distance: 50 - 56: 46.331 distance: 50 - 57: 33.573 distance: 51 - 52: 42.431 distance: 51 - 53: 43.449 distance: 53 - 58: 34.762 distance: 53 - 59: 41.905 distance: 60 - 61: 64.340 distance: 60 - 66: 52.244 distance: 61 - 62: 50.428 distance: 61 - 64: 49.440 distance: 61 - 67: 36.008 distance: 62 - 63: 22.148 distance: 62 - 74: 39.277 distance: 64 - 65: 26.764 distance: 64 - 68: 24.867 distance: 64 - 69: 48.883 distance: 65 - 66: 25.957 distance: 65 - 70: 5.366 distance: 65 - 71: 7.498 distance: 66 - 72: 19.801 distance: 66 - 73: 23.326 distance: 74 - 75: 41.090 distance: 74 - 83: 24.904 distance: 75 - 76: 63.570 distance: 75 - 78: 49.193 distance: 75 - 84: 34.437 distance: 76 - 77: 42.430 distance: 76 - 89: 65.945 distance: 78 - 79: 35.152 distance: 78 - 85: 7.454 distance: 78 - 86: 21.959 distance: 79 - 80: 30.859 distance: 79 - 87: 19.374 distance: 79 - 88: 29.271 distance: 80 - 81: 19.344 distance: 80 - 82: 40.142 distance: 89 - 90: 46.003 distance: 89 - 95: 47.633 distance: 90 - 91: 14.763 distance: 90 - 93: 22.222 distance: 90 - 96: 47.146 distance: 91 - 92: 30.306 distance: 91 - 99: 24.701 distance: 93 - 94: 47.871 distance: 93 - 97: 21.635 distance: 93 - 98: 44.997 distance: 99 - 100: 6.382 distance: 99 - 108: 16.617 distance: 100 - 101: 5.791 distance: 100 - 103: 8.041 distance: 100 - 109: 5.506 distance: 101 - 102: 19.544 distance: 101 - 114: 11.203 distance: 103 - 104: 4.576 distance: 103 - 110: 9.575 distance: 103 - 111: 13.933 distance: 104 - 105: 3.915 distance: 104 - 112: 4.319 distance: 104 - 113: 3.311 distance: 105 - 106: 7.464 distance: 105 - 107: 8.695 distance: 114 - 115: 3.470 distance: 114 - 122: 7.338 distance: 115 - 116: 3.866 distance: 115 - 118: 7.822 distance: 115 - 123: 4.603 distance: 116 - 117: 14.247 distance: 118 - 119: 4.194