Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 01:46:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osl_17160/07_2023/8osl_17160.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osl_17160/07_2023/8osl_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osl_17160/07_2023/8osl_17160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osl_17160/07_2023/8osl_17160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osl_17160/07_2023/8osl_17160.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osl_17160/07_2023/8osl_17160.pdb" } 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 ------------------------------------------------------------------------------- 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/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: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 12} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 11} 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: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 11} 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: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 3} 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: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 12} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 11} 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: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 11} 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: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'HIS:plan': 3} 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: {'GLN:plan1': 12, 'HIS:plan': 13, 'TYR:plan': 16, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 18, 'GLU:plan': 28, 'ARG:plan': 15} 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: {'GLN:plan1': 11, 'HIS:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 14, 'ARG:plan': 23} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 7.30, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 7.64 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 5.41 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: 7.14 Time building geometry restraints manager: 7.90 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=" N GLY N 75 " pdb=" CA GLY N 75 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.00e+00 bond pdb=" N ARG N 245 " pdb=" CA ARG N 245 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.58e+00 bond pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N LEU F 22 " pdb=" CA LEU F 22 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.44e+00 bond pdb=" N ALA P 80 " pdb=" CA ALA P 80 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.28e+00 ... (remaining 14294 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.33: 1261 105.33 - 112.23: 8492 112.23 - 119.13: 3835 119.13 - 126.02: 6823 126.02 - 132.92: 884 Bond angle restraints: 21295 Sorted by residual: angle pdb=" C2' DG I 135 " pdb=" C1' DG I 135 " pdb=" N9 DG I 135 " ideal model delta sigma weight residual 113.50 118.31 -4.81 1.50e+00 4.44e-01 1.03e+01 angle pdb=" O3' DG I 88 " pdb=" C3' DG I 88 " pdb=" C2' DG I 88 " ideal model delta sigma weight residual 111.50 116.05 -4.55 1.50e+00 4.44e-01 9.22e+00 angle pdb=" C4' DA I 97 " pdb=" C3' DA I 97 " pdb=" O3' DA I 97 " ideal model delta sigma weight residual 110.00 114.53 -4.53 1.50e+00 4.44e-01 9.11e+00 angle pdb=" C2' DA I 25 " pdb=" C1' DA I 25 " pdb=" N9 DA I 25 " ideal model delta sigma weight residual 113.50 117.89 -4.39 1.50e+00 4.44e-01 8.55e+00 angle pdb=" C3' DA I 97 " pdb=" O3' DA I 97 " pdb=" P DA I 98 " ideal model delta sigma weight residual 120.20 124.57 -4.37 1.50e+00 4.44e-01 8.49e+00 ... (remaining 21290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 6023 35.19 - 70.38: 1170 70.38 - 105.58: 17 105.58 - 140.77: 1 140.77 - 175.96: 1 Dihedral angle restraints: 7212 sinusoidal: 3063 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 7209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1534 0.042 - 0.085: 683 0.085 - 0.127: 262 0.127 - 0.170: 52 0.170 - 0.212: 8 Chirality restraints: 2539 Sorted by residual: chirality pdb=" CA TRP M 284 " pdb=" N TRP M 284 " pdb=" C TRP M 284 " pdb=" CB TRP M 284 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ARG N 81 " pdb=" N ARG N 81 " pdb=" C ARG N 81 " pdb=" CB ARG N 81 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA GLU M 143 " pdb=" N GLU M 143 " pdb=" C GLU M 143 " pdb=" CB GLU M 143 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.44e-01 ... (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 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: 0.530 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: 0.370 Extract box with map and model: 3.540 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.830 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 : 0.005 0.046 13998 Z= 0.258 Angle : 0.803 5.175 20521 Z= 0.512 Chirality : 0.054 0.212 2539 Planarity : 0.005 0.040 1760 Dihedral : 28.452 175.962 4486 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1280 time to fit residues: 9.7131 Evaluate side-chains 35 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 40.0000 chunk 128 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 153 optimal weight: 1.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 13998 Z= 0.266 Angle : 0.609 6.110 20521 Z= 0.383 Chirality : 0.037 0.141 2539 Planarity : 0.004 0.031 1760 Dihedral : 31.480 178.703 4357 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 41.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1405 helix: 2.16 (0.17), residues: 859 sheet: -0.37 (0.42), residues: 132 loop : 0.16 (0.30), residues: 414 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1200 time to fit residues: 9.2203 Evaluate side-chains 35 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 chunk 127 optimal weight: 40.0000 chunk 104 optimal weight: 40.0000 chunk 42 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 123 optimal weight: 0.0980 overall best weight: 6.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.172 13998 Z= 0.371 Angle : 0.706 5.829 20521 Z= 0.442 Chirality : 0.042 0.185 2539 Planarity : 0.004 0.036 1760 Dihedral : 33.250 175.952 4357 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 74.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1405 helix: 1.59 (0.17), residues: 845 sheet: 0.10 (0.46), residues: 127 loop : -0.24 (0.28), residues: 433 *********************** 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 33 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1228 time to fit residues: 9.0706 Evaluate side-chains 33 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 7.9990 chunk 115 optimal weight: 50.0000 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 154 optimal weight: 30.0000 chunk 163 optimal weight: 50.0000 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 50.0000 chunk 44 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.9828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.102 13998 Z= 0.397 Angle : 0.750 9.364 20521 Z= 0.459 Chirality : 0.044 0.201 2539 Planarity : 0.005 0.046 1760 Dihedral : 35.048 179.117 4357 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 95.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1405 helix: 0.83 (0.18), residues: 854 sheet: 0.05 (0.49), residues: 124 loop : -0.64 (0.28), residues: 427 *********************** 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 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1259 time to fit residues: 8.7726 Evaluate side-chains 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 112 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.9806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 13998 Z= 0.217 Angle : 0.560 5.858 20521 Z= 0.343 Chirality : 0.036 0.127 2539 Planarity : 0.003 0.039 1760 Dihedral : 34.600 177.859 4357 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 61.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1405 helix: 2.05 (0.18), residues: 857 sheet: 0.02 (0.46), residues: 140 loop : -0.48 (0.29), residues: 408 *********************** 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 32 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1293 time to fit residues: 9.0993 Evaluate side-chains 32 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 163 optimal weight: 80.0000 chunk 135 optimal weight: 40.0000 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 157 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 1.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.147 13998 Z= 0.383 Angle : 0.702 7.111 20521 Z= 0.439 Chirality : 0.043 0.209 2539 Planarity : 0.004 0.049 1760 Dihedral : 35.263 177.380 4357 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 98.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1405 helix: 1.22 (0.18), residues: 835 sheet: -0.59 (0.47), residues: 139 loop : -0.71 (0.28), residues: 431 *********************** 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 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1219 time to fit residues: 8.4874 Evaluate side-chains 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 chunk 162 optimal weight: 50.0000 chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 1.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 13998 Z= 0.241 Angle : 0.577 6.119 20521 Z= 0.356 Chirality : 0.037 0.129 2539 Planarity : 0.004 0.043 1760 Dihedral : 34.996 179.653 4357 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 71.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1405 helix: 1.94 (0.18), residues: 844 sheet: -0.47 (0.46), residues: 135 loop : -0.52 (0.29), residues: 426 *********************** 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 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1295 time to fit residues: 8.9948 Evaluate side-chains 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 50.0000 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 148 optimal weight: 50.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 1.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.113 13998 Z= 0.317 Angle : 0.646 7.276 20521 Z= 0.399 Chirality : 0.040 0.171 2539 Planarity : 0.004 0.042 1760 Dihedral : 35.195 179.300 4357 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 93.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1405 helix: 1.72 (0.18), residues: 831 sheet: -0.26 (0.50), residues: 117 loop : -0.93 (0.28), residues: 457 *********************** 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 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.896 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1251 time to fit residues: 8.5113 Evaluate side-chains 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 50.0000 chunk 142 optimal weight: 50.0000 chunk 151 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 0.3980 chunk 137 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 1.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 13998 Z= 0.258 Angle : 0.585 5.860 20521 Z= 0.362 Chirality : 0.037 0.137 2539 Planarity : 0.004 0.041 1760 Dihedral : 35.114 177.027 4357 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 77.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.23), residues: 1405 helix: 2.08 (0.18), residues: 844 sheet: -0.45 (0.50), residues: 117 loop : -0.92 (0.28), residues: 444 *********************** 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 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1314 time to fit residues: 9.1188 Evaluate side-chains 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 0.0060 chunk 168 optimal weight: 50.0000 chunk 154 optimal weight: 50.0000 chunk 134 optimal weight: 50.0000 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 50.0000 chunk 82 optimal weight: 6.9990 chunk 106 optimal weight: 50.0000 chunk 142 optimal weight: 40.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 1.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 13998 Z= 0.304 Angle : 0.612 8.474 20521 Z= 0.379 Chirality : 0.038 0.156 2539 Planarity : 0.004 0.039 1760 Dihedral : 35.123 176.144 4357 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 89.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1405 helix: 1.83 (0.18), residues: 843 sheet: -0.58 (0.50), residues: 117 loop : -1.00 (0.28), residues: 445 ********************** 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 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.395 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1272 time to fit residues: 8.9025 Evaluate side-chains 31 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 50.0000 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 137 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 24 optimal weight: 30.0000 chunk 117 optimal weight: 50.0000 chunk 7 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.067362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.040998 restraints weight = 181326.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038881 restraints weight = 197883.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038534 restraints weight = 218595.907| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 1.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 13998 Z= 0.242 Angle : 0.564 6.179 20521 Z= 0.347 Chirality : 0.036 0.132 2539 Planarity : 0.004 0.043 1760 Dihedral : 34.988 174.129 4357 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 72.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1405 helix: 2.33 (0.18), residues: 844 sheet: -0.69 (0.50), residues: 117 loop : -1.01 (0.28), residues: 444 =============================================================================== Job complete usr+sys time: 1598.07 seconds wall clock time: 30 minutes 32.75 seconds (1832.75 seconds total)