Starting phenix.real_space_refine on Thu May 15 16:20:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osl_17160/05_2025/8osl_17160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osl_17160/05_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_17160/05_2025/8osl_17160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osl_17160/05_2025/8osl_17160.map" model { file = "/net/cci-nas-00/data/ceres_data/8osl_17160/05_2025/8osl_17160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osl_17160/05_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-5687/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: 7.56, per 1000 atoms: 0.56 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: 3.81 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: 5.92 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: 7.57 Time building geometry restraints manager: 4.15 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: 0.430 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: 38.480 Find NCS groups from input model: 0.290 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.110 ------------------------------------------------------------------------------- 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 : 0.925 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1177 time to fit residues: 8.9834 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 : 0.896 ------------------------------------------------------------------------------- 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 = 174507.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041636 restraints weight = 156247.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.041551 restraints weight = 157303.809| |-----------------------------------------------------------------------------| 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 : 1.199 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1243 time to fit residues: 9.1670 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 : 1.078 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 0.9980 chunk 138 optimal weight: 50.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.071631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043141 restraints weight = 180571.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041998 restraints weight = 155243.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041736 restraints weight = 167012.150| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13998 Z= 0.189 Angle : 0.534 5.939 20521 Z= 0.332 Chirality : 0.034 0.127 2539 Planarity : 0.004 0.036 1760 Dihedral : 32.246 177.535 4613 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 42.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 2.20 (0.22), residues: 1405 helix: 2.37 (0.17), residues: 863 sheet: -0.30 (0.42), residues: 144 loop : 0.19 (0.30), residues: 398 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 0.05987 ( 1110) hydrogen bonds : angle 3.63602 ( 2932) covalent geometry : bond 0.00379 (13998) covalent geometry : angle 0.53395 (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 : 1.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1165 time to fit residues: 8.4764 Evaluate side-chains 33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 5.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 40.0000 chunk 143 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 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: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.068372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046450 restraints weight = 190763.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.043558 restraints weight = 309789.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.040211 restraints weight = 259861.028| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.8283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.166 13998 Z= 0.327 Angle : 0.682 6.357 20521 Z= 0.424 Chirality : 0.042 0.170 2539 Planarity : 0.004 0.039 1760 Dihedral : 33.451 174.445 4613 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 78.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.22), residues: 1405 helix: 1.63 (0.17), residues: 868 sheet: -0.04 (0.45), residues: 142 loop : -0.20 (0.30), residues: 395 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 0.10912 ( 1110) hydrogen bonds : angle 4.81041 ( 2932) covalent geometry : bond 0.00674 (13998) covalent geometry : angle 0.68182 (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 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.949 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1207 time to fit residues: 8.4987 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 : 0.954 ------------------------------------------------------------------------------- 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: 0.0870 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 40.0000 chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 148 optimal weight: 50.0000 chunk 147 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 overall best weight: 3.6164 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.069685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047813 restraints weight = 192419.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046098 restraints weight = 311226.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044554 restraints weight = 249966.029| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.8586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13998 Z= 0.221 Angle : 0.558 6.041 20521 Z= 0.345 Chirality : 0.036 0.139 2539 Planarity : 0.004 0.038 1760 Dihedral : 33.403 171.786 4613 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 57.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.23), residues: 1405 helix: 2.28 (0.18), residues: 869 sheet: 0.04 (0.45), residues: 141 loop : -0.31 (0.30), residues: 395 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 0.07296 ( 1110) hydrogen bonds : angle 3.92439 ( 2932) covalent geometry : bond 0.00442 (13998) covalent geometry : angle 0.55797 (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 : 0.951 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1185 time to fit residues: 8.3732 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 : 0.938 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 40.0000 chunk 9 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 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: 4.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.066861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.044951 restraints weight = 199912.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.043528 restraints weight = 277979.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.041758 restraints weight = 224301.483| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 1.0351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 13998 Z= 0.336 Angle : 0.675 8.885 20521 Z= 0.420 Chirality : 0.041 0.199 2539 Planarity : 0.004 0.043 1760 Dihedral : 34.137 178.635 4613 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 87.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: 1.08 (0.22), residues: 1405 helix: 1.48 (0.18), residues: 863 sheet: -0.07 (0.48), residues: 120 loop : -0.55 (0.28), residues: 422 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 0.11646 ( 1110) hydrogen bonds : angle 4.92599 ( 2932) covalent geometry : bond 0.00689 (13998) covalent geometry : angle 0.67525 (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 : 0.997 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1335 time to fit residues: 9.7522 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 : 1.065 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 107 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.066442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.044870 restraints weight = 179928.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.042737 restraints weight = 300471.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.041829 restraints weight = 279881.233| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 1.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 13998 Z= 0.318 Angle : 0.671 9.084 20521 Z= 0.416 Chirality : 0.041 0.180 2539 Planarity : 0.004 0.039 1760 Dihedral : 34.905 174.520 4613 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 80.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: 0.59 (0.22), residues: 1405 helix: 1.29 (0.18), residues: 844 sheet: -0.95 (0.46), residues: 133 loop : -0.87 (0.29), residues: 428 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 0.09842 ( 1110) hydrogen bonds : angle 4.98922 ( 2932) covalent geometry : bond 0.00642 (13998) covalent geometry : angle 0.67065 (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 31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.930 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1176 time to fit residues: 8.0475 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 149 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 50.0000 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.066207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039733 restraints weight = 185431.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.037595 restraints weight = 189232.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037000 restraints weight = 261561.189| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 1.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 13998 Z= 0.298 Angle : 0.645 9.085 20521 Z= 0.400 Chirality : 0.040 0.187 2539 Planarity : 0.004 0.039 1760 Dihedral : 34.807 175.917 4613 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 83.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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: 0.70 (0.23), residues: 1405 helix: 1.41 (0.18), residues: 850 sheet: -0.76 (0.48), residues: 122 loop : -1.01 (0.29), residues: 433 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 0.10031 ( 1110) hydrogen bonds : angle 4.90896 ( 2932) covalent geometry : bond 0.00610 (13998) covalent geometry : angle 0.64489 (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 : 0.981 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1242 time to fit residues: 8.5247 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 : 0.972 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 30.0000 chunk 130 optimal weight: 0.1980 chunk 83 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 158 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 overall best weight: 5.2388 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.066405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.044408 restraints weight = 184259.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.042773 restraints weight = 266044.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041130 restraints weight = 185565.040| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 1.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 13998 Z= 0.300 Angle : 0.657 10.298 20521 Z= 0.405 Chirality : 0.041 0.187 2539 Planarity : 0.004 0.041 1760 Dihedral : 35.129 171.429 4613 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 86.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: 0.82 (0.23), residues: 1405 helix: 1.61 (0.18), residues: 851 sheet: -1.15 (0.50), residues: 117 loop : -1.07 (0.29), residues: 437 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 0.09590 ( 1110) hydrogen bonds : angle 4.88337 ( 2932) covalent geometry : bond 0.00617 (13998) covalent geometry : angle 0.65723 (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 : 1.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1245 time to fit residues: 8.5772 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 : 1.003 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 111 optimal weight: 50.0000 chunk 4 optimal weight: 9.9990 overall best weight: 4.9186 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.066048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039636 restraints weight = 184260.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.037610 restraints weight = 208051.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.037218 restraints weight = 254104.445| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 1.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 13998 Z= 0.284 Angle : 0.631 12.574 20521 Z= 0.389 Chirality : 0.039 0.192 2539 Planarity : 0.004 0.040 1760 Dihedral : 35.010 173.521 4613 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 82.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.23), residues: 1405 helix: 1.68 (0.18), residues: 844 sheet: -0.99 (0.53), residues: 109 loop : -1.26 (0.28), residues: 452 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 0.09556 ( 1110) hydrogen bonds : angle 4.79622 ( 2932) covalent geometry : bond 0.00584 (13998) covalent geometry : angle 0.63102 (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 : 1.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1273 time to fit residues: 8.8442 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 : 0.985 ------------------------------------------------------------------------------- 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: 10.0000 chunk 9 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 150 optimal weight: 50.0000 chunk 122 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 116 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 138 optimal weight: 30.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.063119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037799 restraints weight = 202434.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.036704 restraints weight = 193827.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036345 restraints weight = 199271.627| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 1.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 13998 Z= 0.357 Angle : 0.723 16.159 20521 Z= 0.446 Chirality : 0.044 0.251 2539 Planarity : 0.005 0.045 1760 Dihedral : 35.410 178.018 4613 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 109.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % 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: 0.03 (0.23), residues: 1405 helix: 1.02 (0.18), residues: 850 sheet: -1.16 (0.53), residues: 110 loop : -1.57 (0.28), residues: 445 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 0.12375 ( 1110) hydrogen bonds : angle 5.54008 ( 2932) covalent geometry : bond 0.00736 (13998) covalent geometry : angle 0.72310 (20521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4097.08 seconds wall clock time: 72 minutes 3.31 seconds (4323.31 seconds total)