Starting phenix.real_space_refine on Thu Aug 6 03:51:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osl_17160/08_2026/8osl_17160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osl_17160/08_2026/8osl_17160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8osl_17160/08_2026/8osl_17160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osl_17160/08_2026/8osl_17160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8osl_17160/08_2026/8osl_17160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osl_17160/08_2026/8osl_17160.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.055 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 P 294 5.49 5 C 7188 2.51 5 N 2553 2.21 5 O 3205 1.98 5 H 301 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13541 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 480 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 12, 'TYR:plan': 3, 'GLU:plan': 6, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 173 Chain: "B" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 405 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 11, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 551 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 156 Chain: "D" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 468 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 134 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 480 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 12, 'TYR:plan': 3, 'GLU:plan': 6, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 173 Chain: "F" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 405 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 11, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "G" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 551 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 156 Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 458 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 130 Chain: "I" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2987 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3040 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1665 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 278} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain breaks: 2 Unresolved non-hydrogen bonds: 1058 Unresolved non-hydrogen angles: 1354 Unresolved non-hydrogen dihedrals: 900 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ARG:plan': 15, 'ASN:plan1': 10, 'GLU:plan': 28, 'ASP:plan': 13, 'GLN:plan1': 12, 'PHE:plan': 18, 'HIS:plan': 13, 'TYR:plan': 16, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 625 Chain: "N" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 1500 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 7, 'TRANS': 282} Chain breaks: 4 Unresolved non-hydrogen bonds: 931 Unresolved non-hydrogen angles: 1173 Unresolved non-hydrogen dihedrals: 784 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ARG:plan': 23, 'ASN:plan1': 11, 'GLU:plan': 14, 'HIS:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 15, 'PHE:plan': 16, 'TYR:plan': 9, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 525 Chain: "O" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 292 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "P" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 259 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 3.26, per 1000 atoms: 0.24 Number of scatterers: 13541 At special positions: 0 Unit cell: (137.76, 129.36, 134.4, 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) P 294 15.00 O 3205 8.00 N 2553 7.00 C 7188 6.00 H 301 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 578.6 milliseconds 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2726 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 63.6% alpha, 14.0% beta 147 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.403A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.203A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.198A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 48 through 76 removed outlier: 4.401A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'M' and resid 35 through 60 removed outlier: 3.744A pdb=" N MET M 60 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 90 Processing helix chain 'M' and resid 106 through 119 Processing helix chain 'M' and resid 136 through 143 removed outlier: 4.225A pdb=" N SER M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 150 Processing helix chain 'M' and resid 153 through 157 Processing helix chain 'M' and resid 159 through 161 No H-bonds generated for 'chain 'M' and resid 159 through 161' Processing helix chain 'M' and resid 162 through 173 removed outlier: 4.082A pdb=" N HIS M 173 " --> pdb=" O ILE M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 186 Processing helix chain 'M' and resid 292 through 298 removed outlier: 3.559A pdb=" N ILE M 296 " --> pdb=" O ARG M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 305 removed outlier: 3.597A pdb=" N VAL M 304 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 313 Processing helix chain 'M' and resid 316 through 332 removed outlier: 4.389A pdb=" N ASN M 320 " --> pdb=" O ASP M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 384 Processing helix chain 'N' and resid 76 through 105 removed outlier: 3.505A pdb=" N HIS N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 112 Processing helix chain 'N' and resid 117 through 129 Processing helix chain 'N' and resid 151 through 160 Processing helix chain 'N' and resid 182 through 187 removed outlier: 3.563A pdb=" N ILE N 186 " --> pdb=" O SER N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 195 Processing helix chain 'N' and resid 198 through 203 removed outlier: 4.134A pdb=" N TYR N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 215 removed outlier: 4.448A pdb=" N ALA N 209 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS N 210 " --> pdb=" O LYS N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 368 removed outlier: 3.738A pdb=" N THR N 364 " --> pdb=" O ASP N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 375 removed outlier: 3.543A pdb=" N LEU N 374 " --> pdb=" O LEU N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 378 through 382 Processing helix chain 'N' and resid 384 through 399 removed outlier: 4.425A pdb=" N GLY N 389 " --> pdb=" O GLN N 385 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS N 390 " --> pdb=" O ASP N 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 60 removed outlier: 3.815A pdb=" N MET O 60 " --> pdb=" O GLU O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 90 Processing helix chain 'P' and resid 81 through 106 Processing helix chain 'P' and resid 106 through 112 Processing helix chain 'P' and resid 117 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.944A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.105A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.930A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.285A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 131 through 134 removed outlier: 6.129A pdb=" N ILE M 131 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N MET M 126 " --> pdb=" O ILE M 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 264 through 266 removed outlier: 4.282A pdb=" N TRP M 350 " --> pdb=" O MET M 266 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 286 through 289 removed outlier: 6.032A pdb=" N ARG M 279 " --> pdb=" O LEU M 287 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU M 289 " --> pdb=" O THR M 277 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR M 277 " --> pdb=" O LEU M 289 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE M 368 " --> pdb=" O THR M 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 176 through 179 removed outlier: 6.555A pdb=" N ILE N 176 " --> pdb=" O GLY N 170 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY N 170 " --> pdb=" O ILE N 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 356 through 359 removed outlier: 6.460A pdb=" N ARG N 349 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL N 359 " --> pdb=" O VAL N 347 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL N 347 " --> pdb=" O VAL N 359 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL N 437 " --> pdb=" O ASN N 431 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASN N 431 " --> pdb=" O VAL N 437 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR N 439 " --> pdb=" O PHE N 429 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 356 through 359 removed outlier: 6.460A pdb=" N ARG N 349 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL N 359 " --> pdb=" O VAL N 347 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL N 347 " --> pdb=" O VAL N 359 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL N 437 " --> pdb=" O ASN N 431 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASN N 431 " --> pdb=" O VAL N 437 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR N 439 " --> pdb=" O PHE N 429 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.09: 301 1.09 - 1.22: 70 1.22 - 1.35: 4128 1.35 - 1.48: 4942 1.48 - 1.61: 4858 Bond restraints: 14299 Sorted by residual: bond pdb=" C3' DT I 136 " pdb=" C2' DT I 136 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.70e+01 bond pdb=" C3' DA J 26 " pdb=" O3' DA J 26 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.04e+01 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.04e+01 bond pdb=" C1' DT I 134 " pdb=" N1 DT I 134 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" C3' DT I 78 " pdb=" C2' DT I 78 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.88e+01 ... (remaining 14294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 18955 1.33 - 2.66: 1899 2.66 - 3.99: 293 3.99 - 5.32: 138 5.32 - 6.65: 10 Bond angle restraints: 21295 Sorted by residual: angle pdb=" O5' DA I 25 " pdb=" C5' DA I 25 " pdb=" C4' DA I 25 " ideal model delta sigma weight residual 109.40 113.14 -3.74 8.00e-01 1.56e+00 2.19e+01 angle pdb=" N3 DT I 132 " pdb=" C4 DT I 132 " pdb=" O4 DT I 132 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" O5' DC I 119 " pdb=" C5' DC I 119 " pdb=" C4' DC I 119 " ideal model delta sigma weight residual 109.40 112.95 -3.55 8.00e-01 1.56e+00 1.96e+01 angle pdb=" N3 DT J 104 " pdb=" C4 DT J 104 " pdb=" O4 DT J 104 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" O4' DT I 93 " pdb=" C4' DT I 93 " pdb=" C3' DT I 93 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 21290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 6373 35.19 - 70.38: 1205 70.38 - 105.58: 17 105.58 - 140.77: 1 140.77 - 175.96: 1 Dihedral angle restraints: 7597 sinusoidal: 3448 harmonic: 4149 Sorted by residual: dihedral pdb=" CA ARG N 173 " pdb=" C ARG N 173 " pdb=" N GLY N 174 " pdb=" CA GLY N 174 " ideal model delta harmonic sigma weight residual -180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" C4' DA J 89 " pdb=" C3' DA J 89 " pdb=" O3' DA J 89 " pdb=" P DC J 90 " ideal model delta sinusoidal sigma weight residual -140.00 35.96 -175.96 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ALA M 253 " pdb=" C ALA M 253 " pdb=" N THR M 254 " pdb=" CA THR M 254 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 7594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1534 0.046 - 0.091: 566 0.091 - 0.137: 210 0.137 - 0.182: 194 0.182 - 0.228: 35 Chirality restraints: 2539 Sorted by residual: chirality pdb=" C3' DA I 129 " pdb=" C4' DA I 129 " pdb=" O3' DA I 129 " pdb=" C2' DA I 129 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' DG J 54 " pdb=" C4' DG J 54 " pdb=" O3' DG J 54 " pdb=" C2' DG J 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C3' DC I 130 " pdb=" C4' DC I 130 " pdb=" O3' DC I 130 " pdb=" C2' DC I 130 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2536 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 135 " 0.061 2.00e-02 2.50e+03 2.49e-02 1.86e+01 pdb=" N9 DG I 135 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DG I 135 " -0.019 2.00e-02 2.50e+03 pdb=" N7 DG I 135 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 135 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 135 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 135 " 0.025 2.00e-02 2.50e+03 pdb=" N1 DG I 135 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 135 " -0.009 2.00e-02 2.50e+03 pdb=" N2 DG I 135 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 135 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 135 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 25 " -0.049 2.00e-02 2.50e+03 2.23e-02 1.36e+01 pdb=" N9 DA I 25 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DA I 25 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 25 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 25 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 25 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 25 " -0.013 2.00e-02 2.50e+03 pdb=" N1 DA I 25 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA I 25 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 25 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 25 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 146 " 0.044 2.00e-02 2.50e+03 1.81e-02 9.82e+00 pdb=" N9 DG I 146 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG I 146 " -0.014 2.00e-02 2.50e+03 pdb=" N7 DG I 146 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 146 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 146 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 146 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DG I 146 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 146 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 146 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 146 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 146 " -0.003 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.58: 435 2.58 - 3.09: 9716 3.09 - 3.59: 19245 3.59 - 4.10: 25107 4.10 - 4.60: 33253 Nonbonded interactions: 87756 Sorted by model distance: nonbonded pdb=" HB2 PRO M 294 " pdb=" HD3 PRO M 295 " model vdw 2.078 2.440 nonbonded pdb=" HA PRO M 294 " pdb=" HB3 PRO M 294 " model vdw 2.206 1.952 nonbonded pdb=" HA PRO H 50 " pdb=" HB3 PRO H 50 " model vdw 2.207 1.952 nonbonded pdb=" HA PRO M 204 " pdb=" HB3 PRO M 204 " model vdw 2.209 1.952 nonbonded pdb=" HB3 PRO M 294 " pdb=" HG3 PRO M 294 " model vdw 2.210 1.952 ... (remaining 87751 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 36 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.140 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.007 0.061 13998 Z= 0.630 Angle : 0.903 6.655 20521 Z= 0.711 Chirality : 0.069 0.228 2539 Planarity : 0.005 0.040 1760 Dihedral : 28.012 175.962 4742 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1405 helix: 0.28 (0.16), residues: 846 sheet: -0.44 (0.40), residues: 140 loop : -0.25 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.63 (13998) covalent geometry : angle 0.90257 / 0.71 (20521) hydrogen bonds : bond 0.11086 / 8.37 ( 1110) hydrogen bonds : angle 5.19816 / 4.11 ( 2932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.343 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0603 time to fit residues: 4.4504 Evaluate side-chains 35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 overall best weight: 8.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.072243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.044239 restraints weight = 178225.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.043029 restraints weight = 146104.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042449 restraints weight = 159912.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042400 restraints weight = 164960.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.042469 restraints weight = 157643.659| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 13998 Z= 0.353 Angle : 0.971 12.511 20521 Z= 0.583 Chirality : 0.060 0.347 2539 Planarity : 0.007 0.053 1760 Dihedral : 32.083 167.477 4613 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 64.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1405 helix: -0.25 (0.17), residues: 840 sheet: -0.11 (0.42), residues: 141 loop : -0.48 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.35 (13998) covalent geometry : angle 0.97133 / 0.58 (20521) hydrogen bonds : bond 0.20252 / 15.75 ( 1110) hydrogen bonds : angle 5.31979 / 4.20 ( 2932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.349 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0602 time to fit residues: 4.4338 Evaluate side-chains 35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 0.4980 chunk 67 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 43 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.075372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044603 restraints weight = 181382.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043488 restraints weight = 172374.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043516 restraints weight = 164133.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043540 restraints weight = 151422.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043557 restraints weight = 143496.760| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13998 Z= 0.152 Angle : 0.609 6.391 20521 Z= 0.385 Chirality : 0.043 0.203 2539 Planarity : 0.004 0.042 1760 Dihedral : 31.576 171.987 4613 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 28.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.22), residues: 1405 helix: 2.12 (0.17), residues: 846 sheet: 0.03 (0.43), residues: 142 loop : 0.15 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.15 (13998) covalent geometry : angle 0.60925 / 0.38 (20521) hydrogen bonds : bond 0.05051 / 3.91 ( 1110) hydrogen bonds : angle 3.80591 / 3.01 ( 2932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0592 time to fit residues: 4.4196 Evaluate side-chains 35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 chunk 71 optimal weight: 50.0000 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 83 optimal weight: 40.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.070774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043495 restraints weight = 174289.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042449 restraints weight = 152050.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.042219 restraints weight = 156898.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.042207 restraints weight = 156808.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.042247 restraints weight = 142593.803| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13998 Z= 0.283 Angle : 0.691 7.193 20521 Z= 0.452 Chirality : 0.043 0.250 2539 Planarity : 0.005 0.046 1760 Dihedral : 31.939 174.779 4613 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 55.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.23), residues: 1405 helix: 1.73 (0.18), residues: 848 sheet: 0.14 (0.45), residues: 140 loop : -0.01 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.28 (13998) covalent geometry : angle 0.69149 / 0.45 (20521) hydrogen bonds : bond 0.12893 / 10.03 ( 1110) hydrogen bonds : angle 4.31659 / 3.40 ( 2932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0599 time to fit residues: 4.1270 Evaluate side-chains 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 151 optimal weight: 50.0000 chunk 23 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 50.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.070655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044747 restraints weight = 182773.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042807 restraints weight = 177093.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.042466 restraints weight = 205526.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042211 restraints weight = 225626.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.042202 restraints weight = 200277.406| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13998 Z= 0.211 Angle : 0.658 6.332 20521 Z= 0.414 Chirality : 0.045 0.217 2539 Planarity : 0.004 0.046 1760 Dihedral : 32.794 175.887 4613 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 47.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.23), residues: 1405 helix: 1.86 (0.18), residues: 852 sheet: 0.10 (0.47), residues: 133 loop : -0.02 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.21 (13998) covalent geometry : angle 0.65832 / 0.41 (20521) hydrogen bonds : bond 0.07102 / 5.52 ( 1110) hydrogen bonds : angle 4.16086 / 3.29 ( 2932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0596 time to fit residues: 4.1421 Evaluate side-chains 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 144 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 162 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 155 optimal weight: 40.0000 chunk 136 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 overall best weight: 9.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.067474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.040523 restraints weight = 185580.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039275 restraints weight = 162040.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038814 restraints weight = 180340.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038790 restraints weight = 199108.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.038792 restraints weight = 179451.251| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 13998 Z= 0.377 Angle : 0.859 9.393 20521 Z= 0.539 Chirality : 0.051 0.287 2539 Planarity : 0.006 0.053 1760 Dihedral : 33.398 178.266 4613 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 87.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1405 helix: 0.53 (0.18), residues: 857 sheet: 0.41 (0.55), residues: 101 loop : -0.62 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.38 (13998) covalent geometry : angle 0.85895 / 0.54 (20521) hydrogen bonds : bond 0.15424 / 12.00 ( 1110) hydrogen bonds : angle 5.45309 / 4.31 ( 2932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.356 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0595 time to fit residues: 4.1372 Evaluate side-chains 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 124 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 145 optimal weight: 50.0000 chunk 74 optimal weight: 30.0000 chunk 113 optimal weight: 50.0000 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 50.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.065524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039769 restraints weight = 195987.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037953 restraints weight = 220819.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037867 restraints weight = 220862.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037812 restraints weight = 200057.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037812 restraints weight = 187768.202| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.9325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 13998 Z= 0.374 Angle : 0.930 8.079 20521 Z= 0.570 Chirality : 0.057 0.296 2539 Planarity : 0.007 0.060 1760 Dihedral : 35.065 179.193 4613 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 117.31 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.90 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.22), residues: 1405 helix: -1.02 (0.18), residues: 837 sheet: -0.37 (0.54), residues: 102 loop : -1.39 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.37 (13998) covalent geometry : angle 0.92959 / 0.57 (20521) hydrogen bonds : bond 0.17819 / 13.80 ( 1110) hydrogen bonds : angle 6.46715 / 5.14 ( 2932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.349 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0604 time to fit residues: 4.0708 Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 10 optimal weight: 0.1980 chunk 168 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.068217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046388 restraints weight = 188163.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.043683 restraints weight = 269091.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040463 restraints weight = 249185.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040463 restraints weight = 232541.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.040456 restraints weight = 206587.292| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.9109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 13998 Z= 0.205 Angle : 0.706 6.942 20521 Z= 0.431 Chirality : 0.046 0.228 2539 Planarity : 0.004 0.038 1760 Dihedral : 34.876 177.820 4613 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 68.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1405 helix: 0.26 (0.18), residues: 863 sheet: -1.08 (0.49), residues: 127 loop : -1.15 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.21 (13998) covalent geometry : angle 0.70586 / 0.43 (20521) hydrogen bonds : bond 0.08988 / 6.98 ( 1110) hydrogen bonds : angle 5.17395 / 4.09 ( 2932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0561 time to fit residues: 3.7023 Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 32 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 chunk 72 optimal weight: 50.0000 chunk 107 optimal weight: 40.0000 chunk 11 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 30.0000 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 0.0030 chunk 129 optimal weight: 50.0000 chunk 114 optimal weight: 0.0470 overall best weight: 1.2690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.070642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048471 restraints weight = 193060.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047131 restraints weight = 275484.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045784 restraints weight = 220584.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.044959 restraints weight = 226273.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044908 restraints weight = 219580.587| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.8841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13998 Z= 0.156 Angle : 0.611 5.831 20521 Z= 0.375 Chirality : 0.043 0.186 2539 Planarity : 0.004 0.037 1760 Dihedral : 34.352 165.832 4613 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 48.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1405 helix: 2.24 (0.18), residues: 874 sheet: -0.97 (0.46), residues: 129 loop : -0.69 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.16 (13998) covalent geometry : angle 0.61083 / 0.37 (20521) hydrogen bonds : bond 0.05538 / 4.30 ( 1110) hydrogen bonds : angle 3.94923 / 3.10 ( 2932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0503 time to fit residues: 3.3864 Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 77 optimal weight: 30.0000 chunk 43 optimal weight: 0.0770 chunk 85 optimal weight: 50.0000 chunk 99 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.0070 chunk 126 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 133 optimal weight: 40.0000 chunk 61 optimal weight: 20.0000 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.070864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048656 restraints weight = 192158.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.047178 restraints weight = 275208.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.044961 restraints weight = 192532.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044304 restraints weight = 262505.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.044243 restraints weight = 219136.007| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.8806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13998 Z= 0.146 Angle : 0.561 6.638 20521 Z= 0.352 Chirality : 0.039 0.178 2539 Planarity : 0.004 0.044 1760 Dihedral : 33.889 157.930 4613 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 46.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.24), residues: 1405 helix: 3.13 (0.18), residues: 871 sheet: -0.66 (0.51), residues: 115 loop : -0.50 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.15 (13998) covalent geometry : angle 0.56093 / 0.35 (20521) hydrogen bonds : bond 0.05171 / 4.00 ( 1110) hydrogen bonds : angle 3.58827 / 2.82 ( 2932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.350 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0512 time to fit residues: 3.3924 Evaluate side-chains 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 129 optimal weight: 40.0000 chunk 105 optimal weight: 20.0000 chunk 153 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 118 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 chunk 115 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 109 optimal weight: 0.0370 chunk 120 optimal weight: 4.9990 overall best weight: 8.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.044000 restraints weight = 195787.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.042943 restraints weight = 281342.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.041911 restraints weight = 248095.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.041314 restraints weight = 250528.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.041188 restraints weight = 229557.497| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 1.0029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 13998 Z= 0.323 Angle : 0.759 8.616 20521 Z= 0.482 Chirality : 0.047 0.239 2539 Planarity : 0.005 0.048 1760 Dihedral : 34.274 166.661 4613 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 98.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1405 helix: 0.80 (0.18), residues: 866 sheet: -0.45 (0.50), residues: 117 loop : -1.22 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.32 (13998) covalent geometry : angle 0.75881 / 0.48 (20521) hydrogen bonds : bond 0.16956 / 13.18 ( 1110) hydrogen bonds : angle 5.14587 / 4.08 ( 2932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.66 seconds wall clock time: 44 minutes 11.29 seconds (2651.29 seconds total)