Starting phenix.real_space_refine on Thu Jul 31 09:52:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osl_17160/07_2025/8osl_17160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osl_17160/07_2025/8osl_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/cci-nas-00/data/ceres_data/8osl_17160/07_2025/8osl_17160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osl_17160/07_2025/8osl_17160.map" model { file = "/net/cci-nas-00/data/ceres_data/8osl_17160/07_2025/8osl_17160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osl_17160/07_2025/8osl_17160.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.79, per 1000 atoms: 0.58 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: 3.21 Conformation dependent library (CDL) restraints added in 1.4 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: 6.64 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: 7.34 Time building geometry restraints manager: 3.84 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: 0.00 - 1.04: 17986 1.04 - 2.07: 2573 2.07 - 3.11: 606 3.11 - 4.14: 118 4.14 - 5.18: 12 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: 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 - 0.042: 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 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: 0.580 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: 0.350 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 38.820 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- 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= 0.236 Angle : 0.803 5.175 20521 Z= 0.512 Chirality : 0.054 0.212 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.11086 ( 1110) hydrogen bonds : angle 5.19816 ( 2932) covalent geometry : bond 0.00479 (13998) covalent geometry : angle 0.80332 (20521) *********************** 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 : 0.978 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1217 time to fit residues: 9.4046 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 : 0.991 ------------------------------------------------------------------------------- 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: 30.0000 chunk 128 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 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: 4.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.070184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042694 restraints weight = 174507.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041636 restraints weight = 156218.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.041552 restraints weight = 157067.608| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 13998 Z= 0.374 Angle : 0.765 7.219 20521 Z= 0.480 Chirality : 0.044 0.214 2539 Planarity : 0.005 0.042 1760 Dihedral : 32.268 179.129 4613 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 66.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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 (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: 0.67 (0.21), residues: 1405 helix: 0.93 (0.17), residues: 852 sheet: -0.55 (0.39), residues: 142 loop : 0.06 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.12459 ( 1110) hydrogen bonds : angle 5.03462 ( 2932) covalent geometry : bond 0.00783 (13998) covalent geometry : angle 0.76550 (20521) *********************** 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 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.154 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1378 time to fit residues: 9.8951 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 : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 138 optimal weight: 50.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.072021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043406 restraints weight = 182449.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042433 restraints weight = 152843.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042216 restraints weight = 152656.671| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13998 Z= 0.184 Angle : 0.536 5.948 20521 Z= 0.331 Chirality : 0.034 0.141 2539 Planarity : 0.004 0.035 1760 Dihedral : 32.195 177.383 4613 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 41.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.23), residues: 1405 helix: 2.50 (0.17), residues: 865 sheet: -0.29 (0.42), residues: 144 loop : 0.19 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 1110) hydrogen bonds : angle 3.53171 ( 2932) covalent geometry : bond 0.00365 (13998) covalent geometry : angle 0.53648 (20521) *********************** 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 to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1251 time to fit residues: 9.1865 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 : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 128 optimal weight: 8.9990 chunk 27 optimal weight: 0.0970 chunk 17 optimal weight: 30.0000 chunk 143 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 135 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.068132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.040540 restraints weight = 185695.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039470 restraints weight = 159055.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.038942 restraints weight = 188191.296| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.7970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.163 13998 Z= 0.317 Angle : 0.662 6.385 20521 Z= 0.409 Chirality : 0.041 0.156 2539 Planarity : 0.004 0.037 1760 Dihedral : 33.247 174.926 4613 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 74.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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 (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: 1.68 (0.22), residues: 1405 helix: 1.88 (0.18), residues: 869 sheet: 0.07 (0.45), residues: 142 loop : -0.11 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.10014 ( 1110) hydrogen bonds : angle 4.62125 ( 2932) covalent geometry : bond 0.00656 (13998) covalent geometry : angle 0.66219 (20521) *********************** 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 : 1.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1211 time to fit residues: 8.8498 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 : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 138 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 50.0000 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 148 optimal weight: 50.0000 chunk 147 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.069923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.048042 restraints weight = 190637.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043719 restraints weight = 260932.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040814 restraints weight = 214279.887| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.8504 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= 0.223 Angle : 0.549 6.189 20521 Z= 0.340 Chirality : 0.035 0.127 2539 Planarity : 0.004 0.035 1760 Dihedral : 33.319 170.323 4613 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 55.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.23), residues: 1405 helix: 2.45 (0.18), residues: 869 sheet: 0.07 (0.45), residues: 142 loop : -0.23 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.07047 ( 1110) hydrogen bonds : angle 3.79055 ( 2932) covalent geometry : bond 0.00445 (13998) covalent geometry : angle 0.54859 (20521) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.561 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2686 time to fit residues: 18.2320 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 : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 50.0000 chunk 121 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.064827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.043255 restraints weight = 203418.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.042079 restraints weight = 287558.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.040750 restraints weight = 234815.699| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 1.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.208 13998 Z= 0.478 Angle : 0.855 14.678 20521 Z= 0.536 Chirality : 0.050 0.285 2539 Planarity : 0.006 0.049 1760 Dihedral : 34.931 176.046 4613 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 115.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.40 % Favored : 92.46 % 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 (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: -0.33 (0.22), residues: 1405 helix: 0.32 (0.18), residues: 834 sheet: -0.52 (0.47), residues: 125 loop : -0.94 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.14834 ( 1110) hydrogen bonds : angle 6.22049 ( 2932) covalent geometry : bond 0.00971 (13998) covalent geometry : angle 0.85498 (20521) *********************** 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 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.585 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1456 time to fit residues: 10.2433 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 : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 99 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 106 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 107 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.067280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.045024 restraints weight = 198303.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.043883 restraints weight = 263380.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.042505 restraints weight = 211034.847| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 1.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 13998 Z= 0.247 Angle : 0.604 9.707 20521 Z= 0.371 Chirality : 0.038 0.148 2539 Planarity : 0.004 0.040 1760 Dihedral : 34.621 173.278 4613 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 66.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % 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 (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: 0.75 (0.23), residues: 1405 helix: 1.29 (0.18), residues: 864 sheet: -0.78 (0.45), residues: 142 loop : -0.61 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.08520 ( 1110) hydrogen bonds : angle 4.58558 ( 2932) covalent geometry : bond 0.00511 (13998) covalent geometry : angle 0.60418 (20521) *********************** 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 : 1.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1394 time to fit residues: 9.8936 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 149 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 50.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.066568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040363 restraints weight = 180960.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038329 restraints weight = 183821.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.037988 restraints weight = 215774.651| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 1.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 13998 Z= 0.299 Angle : 0.637 10.718 20521 Z= 0.394 Chirality : 0.040 0.182 2539 Planarity : 0.004 0.046 1760 Dihedral : 34.721 177.379 4613 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 79.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % 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 (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: 0.73 (0.23), residues: 1405 helix: 1.31 (0.18), residues: 864 sheet: -0.82 (0.46), residues: 132 loop : -0.71 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.09592 ( 1110) hydrogen bonds : angle 4.92048 ( 2932) covalent geometry : bond 0.00611 (13998) covalent geometry : angle 0.63712 (20521) *********************** 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 to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.576 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1866 time to fit residues: 13.6141 Evaluate side-chains 31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 0.0370 chunk 105 optimal weight: 40.0000 chunk 130 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 158 optimal weight: 30.0000 chunk 143 optimal weight: 50.0000 overall best weight: 2.5464 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.068313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047016 restraints weight = 179688.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043642 restraints weight = 266177.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040208 restraints weight = 205260.622| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 1.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13998 Z= 0.195 Angle : 0.544 6.034 20521 Z= 0.333 Chirality : 0.035 0.140 2539 Planarity : 0.004 0.043 1760 Dihedral : 34.319 168.761 4613 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 58.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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 (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: 1.83 (0.23), residues: 1405 helix: 2.34 (0.18), residues: 868 sheet: -0.62 (0.47), residues: 129 loop : -0.65 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.06432 ( 1110) hydrogen bonds : angle 3.95036 ( 2932) covalent geometry : bond 0.00396 (13998) covalent geometry : angle 0.54385 (20521) *********************** 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 to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.963 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1281 time to fit residues: 8.8953 Evaluate side-chains 31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 161 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 118 optimal weight: 0.0470 chunk 20 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 104 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.066176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.044265 restraints weight = 182421.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041896 restraints weight = 274890.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038946 restraints weight = 206753.666| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 1.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 13998 Z= 0.306 Angle : 0.639 11.424 20521 Z= 0.395 Chirality : 0.040 0.181 2539 Planarity : 0.004 0.043 1760 Dihedral : 34.717 177.652 4613 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 85.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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 (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: 1.14 (0.23), residues: 1405 helix: 1.88 (0.18), residues: 844 sheet: -1.22 (0.47), residues: 132 loop : -0.81 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.09948 ( 1110) hydrogen bonds : angle 4.84048 ( 2932) covalent geometry : bond 0.00626 (13998) covalent geometry : angle 0.63901 (20521) ********************** 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 to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.942 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1253 time to fit residues: 8.5481 Evaluate side-chains 31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 20.0000 chunk 165 optimal weight: 50.0000 chunk 28 optimal weight: 0.3980 chunk 150 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 32 optimal weight: 30.0000 chunk 116 optimal weight: 40.0000 chunk 54 optimal weight: 0.2980 chunk 139 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 overall best weight: 8.2588 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.063968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038540 restraints weight = 195012.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.036265 restraints weight = 221855.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.035896 restraints weight = 265887.623| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 1.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 13998 Z= 0.454 Angle : 0.839 18.083 20521 Z= 0.525 Chirality : 0.050 0.337 2539 Planarity : 0.005 0.045 1760 Dihedral : 35.754 178.478 4613 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 134.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.04 % Favored : 90.82 % 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 (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: -0.84 (0.22), residues: 1405 helix: 0.17 (0.18), residues: 830 sheet: -1.39 (0.54), residues: 93 loop : -1.55 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.14659 ( 1110) hydrogen bonds : angle 6.45256 ( 2932) covalent geometry : bond 0.00914 (13998) covalent geometry : angle 0.83866 (20521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4641.50 seconds wall clock time: 82 minutes 49.26 seconds (4969.26 seconds total)