Starting phenix.real_space_refine on Mon Dec 30 14:50:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osl_17160/12_2024/8osl_17160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osl_17160/12_2024/8osl_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_17160/12_2024/8osl_17160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osl_17160/12_2024/8osl_17160.map" model { file = "/net/cci-nas-00/data/ceres_data/8osl_17160/12_2024/8osl_17160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osl_17160/12_2024/8osl_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-5532/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: 8.26, per 1000 atoms: 0.61 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: 4.00 Conformation dependent library (CDL) restraints added in 1.6 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: 6.72 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: 7.62 Time building geometry restraints manager: 4.36 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: 0.450 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: 0.380 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.750 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13998 Z= 0.258 Angle : 0.803 5.175 20521 Z= 0.512 Chirality : 0.054 0.212 2539 Planarity : 0.005 0.040 1760 Dihedral : 28.012 175.962 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 *********************** 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 : 1.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1204 time to fit residues: 9.3003 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 : 1.049 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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= 0.412 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 *********************** 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 : 0.982 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1215 time to fit residues: 8.9077 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 : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 104 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 166 optimal weight: 30.0000 chunk 136 optimal weight: 30.0000 chunk 152 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 overall best weight: 15.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 1.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.273 13998 Z= 0.773 Angle : 1.180 15.450 20521 Z= 0.732 Chirality : 0.067 0.361 2539 Planarity : 0.009 0.074 1760 Dihedral : 36.251 174.477 4613 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 178.43 Ramachandran Plot: Outliers : 0.78 % Allowed : 13.31 % Favored : 85.91 % 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 : 0.14 % 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: -2.81 (0.21), residues: 1405 helix: -1.98 (0.17), residues: 799 sheet: -0.19 (0.51), residues: 104 loop : -1.72 (0.26), residues: 502 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 *********************** 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 32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1418 time to fit residues: 9.9977 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 : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 40.0000 chunk 115 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 50.0000 chunk 154 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 1.0324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 13998 Z= 0.299 Angle : 0.685 7.477 20521 Z= 0.420 Chirality : 0.041 0.171 2539 Planarity : 0.005 0.048 1760 Dihedral : 35.689 170.499 4613 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 74.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: -1.52 (0.22), residues: 1405 helix: -0.77 (0.18), residues: 849 sheet: -0.78 (0.46), residues: 132 loop : -1.19 (0.29), residues: 424 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 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1302 time to fit residues: 8.9159 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 : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 50.0000 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 139 optimal weight: 50.0000 chunk 112 optimal weight: 40.0000 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 146 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 1.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 13998 Z= 0.346 Angle : 0.680 9.289 20521 Z= 0.418 Chirality : 0.042 0.179 2539 Planarity : 0.005 0.053 1760 Dihedral : 35.410 154.716 4613 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 87.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % 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: -0.99 (0.22), residues: 1405 helix: -0.21 (0.18), residues: 853 sheet: -0.96 (0.45), residues: 139 loop : -1.20 (0.29), residues: 413 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 *********************** 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 31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.927 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1554 time to fit residues: 10.0855 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 : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 10.0000 chunk 147 optimal weight: 30.0000 chunk 32 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 1.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.154 13998 Z= 0.466 Angle : 0.822 10.934 20521 Z= 0.513 Chirality : 0.050 0.301 2539 Planarity : 0.006 0.058 1760 Dihedral : 36.014 158.488 4613 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 123.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -1.84 (0.22), residues: 1405 helix: -0.70 (0.18), residues: 830 sheet: -1.75 (0.46), residues: 119 loop : -1.77 (0.27), residues: 456 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 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1257 time to fit residues: 8.7453 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 : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 119 optimal weight: 30.0000 chunk 92 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 162 optimal weight: 40.0000 chunk 101 optimal weight: 30.0000 chunk 99 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 1.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13998 Z= 0.230 Angle : 0.617 6.905 20521 Z= 0.375 Chirality : 0.038 0.147 2539 Planarity : 0.004 0.058 1760 Dihedral : 35.551 157.764 4613 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 64.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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: -0.34 (0.23), residues: 1405 helix: 0.56 (0.18), residues: 855 sheet: -1.37 (0.45), residues: 138 loop : -1.30 (0.30), residues: 412 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 *********************** 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 : 1.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1315 time to fit residues: 9.0090 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 : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 40.0000 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 148 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 1.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 13998 Z= 0.304 Angle : 0.650 10.263 20521 Z= 0.399 Chirality : 0.040 0.171 2539 Planarity : 0.004 0.056 1760 Dihedral : 35.446 156.172 4613 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 83.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % 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: -0.18 (0.23), residues: 1405 helix: 0.69 (0.18), residues: 858 sheet: -1.32 (0.48), residues: 128 loop : -1.28 (0.29), 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 *********************** 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 : 0.994 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1247 time to fit residues: 8.6589 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 : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 40.0000 chunk 142 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 1.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13998 Z= 0.263 Angle : 0.608 8.389 20521 Z= 0.373 Chirality : 0.038 0.143 2539 Planarity : 0.004 0.064 1760 Dihedral : 35.292 157.938 4613 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 72.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % 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: 0.29 (0.23), residues: 1405 helix: 1.18 (0.19), residues: 856 sheet: -1.55 (0.47), residues: 126 loop : -1.22 (0.29), residues: 423 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 *********************** 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 : 1.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1332 time to fit residues: 9.2078 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 : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 168 optimal weight: 50.0000 chunk 154 optimal weight: 20.0000 chunk 134 optimal weight: 50.0000 chunk 13 optimal weight: 0.6980 chunk 103 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 142 optimal weight: 30.0000 overall best weight: 6.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 1.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 13998 Z= 0.366 Angle : 0.704 15.358 20521 Z= 0.435 Chirality : 0.043 0.237 2539 Planarity : 0.005 0.069 1760 Dihedral : 35.603 158.825 4613 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 99.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % 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: -0.36 (0.23), residues: 1405 helix: 0.67 (0.19), residues: 854 sheet: -1.78 (0.46), residues: 133 loop : -1.46 (0.29), residues: 418 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 ********************** 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 : 1.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1261 time to fit residues: 8.6459 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 : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 134 optimal weight: 50.0000 chunk 56 optimal weight: 0.9980 chunk 137 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.063112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.037454 restraints weight = 199296.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036319 restraints weight = 174277.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036303 restraints weight = 176256.728| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 1.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 13998 Z= 0.353 Angle : 0.709 15.108 20521 Z= 0.438 Chirality : 0.043 0.228 2539 Planarity : 0.005 0.074 1760 Dihedral : 35.882 158.028 4613 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 99.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % 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: -0.63 (0.23), residues: 1405 helix: 0.44 (0.18), residues: 848 sheet: -1.57 (0.50), residues: 115 loop : -1.65 (0.29), residues: 442 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.54 seconds wall clock time: 32 minutes 24.05 seconds (1944.05 seconds total)