Starting phenix.real_space_refine on Fri Dec 8 19:44:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/12_2023/7ezm_31389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/12_2023/7ezm_31389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/12_2023/7ezm_31389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/12_2023/7ezm_31389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/12_2023/7ezm_31389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/12_2023/7ezm_31389_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5748 2.51 5 N 1524 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 191": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9008 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1850 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2362 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.94, per 1000 atoms: 0.66 Number of scatterers: 9008 At special positions: 0 Unit cell: (104.5, 120.175, 121.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1667 8.00 N 1524 7.00 C 5748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 35.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 7 through 37 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 235 removed outlier: 3.953A pdb=" N TYR A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.550A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 276 through 284 removed outlier: 4.733A pdb=" N MET A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 302 through 316 removed outlier: 4.347A pdb=" N LEU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 355 removed outlier: 3.903A pdb=" N ILE A 337 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 4.209A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'D' and resid 40 through 68 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 75 through 104 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 144 Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 155 through 179 Proline residue: D 175 - end of helix removed outlier: 3.595A pdb=" N ILE D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 219 through 247 Processing helix chain 'D' and resid 302 through 338 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 350 through 370 removed outlier: 4.019A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.849A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.205A pdb=" N VAL A 269 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS A 327 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 271 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 200 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 42 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG A 202 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 44 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 204 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY A 46 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.882A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.675A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.480A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.814A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.613A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.235A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.631A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 182 through 186 Processing sheet with id= J, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.257A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.476A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 155 through 160 426 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2088 1.33 - 1.46: 2829 1.46 - 1.60: 4172 1.60 - 1.73: 1 1.73 - 1.86: 106 Bond restraints: 9196 Sorted by residual: bond pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.462 1.636 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.526 0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.532 1.465 0.066 1.78e-02 3.16e+03 1.39e+01 bond pdb=" N VAL A 240 " pdb=" CA VAL A 240 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.60e+00 bond pdb=" N GLY B 41 " pdb=" CA GLY B 41 " ideal model delta sigma weight residual 1.448 1.492 -0.044 1.88e-02 2.83e+03 5.56e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.24: 169 105.24 - 112.62: 4599 112.62 - 120.01: 3548 120.01 - 127.39: 4068 127.39 - 134.78: 100 Bond angle restraints: 12484 Sorted by residual: angle pdb=" C ARG D 139 " pdb=" CA ARG D 139 " pdb=" CB ARG D 139 " ideal model delta sigma weight residual 110.68 118.72 -8.04 1.70e+00 3.46e-01 2.23e+01 angle pdb=" C ARG D 345 " pdb=" CA ARG D 345 " pdb=" CB ARG D 345 " ideal model delta sigma weight residual 110.88 103.83 7.05 1.57e+00 4.06e-01 2.02e+01 angle pdb=" N VAL A 238 " pdb=" CA VAL A 238 " pdb=" C VAL A 238 " ideal model delta sigma weight residual 109.20 102.41 6.79 1.55e+00 4.16e-01 1.92e+01 angle pdb=" N ALA H 136 " pdb=" CA ALA H 136 " pdb=" C ALA H 136 " ideal model delta sigma weight residual 113.02 107.99 5.03 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA VAL A 238 " pdb=" C VAL A 238 " pdb=" O VAL A 238 " ideal model delta sigma weight residual 121.92 117.04 4.88 1.17e+00 7.31e-01 1.74e+01 ... (remaining 12479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4939 16.36 - 32.71: 413 32.71 - 49.06: 76 49.06 - 65.42: 22 65.42 - 81.77: 5 Dihedral angle restraints: 5455 sinusoidal: 2051 harmonic: 3404 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1137 0.081 - 0.163: 272 0.163 - 0.244: 23 0.244 - 0.325: 3 0.325 - 0.407: 2 Chirality restraints: 1437 Sorted by residual: chirality pdb=" CA ARG A 210 " pdb=" N ARG A 210 " pdb=" C ARG A 210 " pdb=" CB ARG A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA ARG D 345 " pdb=" N ARG D 345 " pdb=" C ARG D 345 " pdb=" CB ARG D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1434 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 313 " 0.048 9.50e-02 1.11e+02 4.23e-02 1.69e+01 pdb=" NE ARG D 313 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG D 313 " 0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG D 313 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG D 313 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 367 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PRO D 367 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO D 367 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE D 368 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 202 " -0.006 9.50e-02 1.11e+02 3.17e-02 1.25e+01 pdb=" NE ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 202 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 202 " 0.020 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1306 2.76 - 3.30: 9258 3.30 - 3.83: 15488 3.83 - 4.37: 19207 4.37 - 4.90: 32183 Nonbonded interactions: 77442 Sorted by model distance: nonbonded pdb=" OH TYR A 356 " pdb=" OE1 GLN D 153 " model vdw 2.228 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 2.440 nonbonded pdb=" O TYR D 360 " pdb=" OG SER D 363 " model vdw 2.247 2.440 nonbonded pdb=" O MET D 72 " pdb=" ND2 ASN D 77 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.260 2.440 ... (remaining 77437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.670 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: 0.020 Extract box with map and model: 3.850 Check model and map are aligned: 0.140 Set scattering table: 0.000 Process input model: 32.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.011 0.174 9196 Z= 0.698 Angle : 1.074 9.054 12484 Z= 0.645 Chirality : 0.068 0.407 1437 Planarity : 0.009 0.102 1576 Dihedral : 13.160 81.772 3241 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.94 % Allowed : 3.34 % Favored : 95.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % 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: -0.87 (0.23), residues: 1150 helix: -0.43 (0.23), residues: 404 sheet: -0.10 (0.30), residues: 278 loop : -0.83 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP B 82 HIS 0.019 0.006 HIS D 157 PHE 0.025 0.006 PHE B 241 TYR 0.046 0.009 TYR H 175 ARG 0.071 0.009 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 308 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 315 average time/residue: 1.0943 time to fit residues: 369.5731 Evaluate side-chains 274 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 270 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.4019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0570 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.0060 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 220 GLN D 374 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.182 Angle : 0.592 6.342 12484 Z= 0.310 Chirality : 0.043 0.155 1437 Planarity : 0.005 0.047 1576 Dihedral : 5.830 73.335 1262 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 5.11 % Allowed : 13.88 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.56 (0.25), residues: 1150 helix: 1.34 (0.26), residues: 407 sheet: -0.15 (0.30), residues: 278 loop : -0.02 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS B 62 PHE 0.034 0.002 PHE A 55 TYR 0.012 0.001 TYR D 179 ARG 0.008 0.001 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 266 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 23 residues processed: 286 average time/residue: 1.0800 time to fit residues: 331.7580 Evaluate side-chains 271 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 12 residues processed: 11 average time/residue: 0.5394 time to fit residues: 8.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN D 374 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9196 Z= 0.215 Angle : 0.571 6.576 12484 Z= 0.296 Chirality : 0.043 0.141 1437 Planarity : 0.004 0.049 1576 Dihedral : 5.397 69.655 1262 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.49 % Allowed : 18.06 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1150 helix: 1.42 (0.26), residues: 408 sheet: -0.15 (0.29), residues: 282 loop : 0.15 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS B 62 PHE 0.034 0.002 PHE H 68 TYR 0.015 0.001 TYR D 179 ARG 0.010 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 244 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 268 average time/residue: 1.1414 time to fit residues: 328.2178 Evaluate side-chains 253 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 8 average time/residue: 0.3963 time to fit residues: 5.0360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN D 44 GLN D 304 ASN D 366 ASN H 39 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9196 Z= 0.313 Angle : 0.591 7.233 12484 Z= 0.307 Chirality : 0.044 0.176 1437 Planarity : 0.004 0.049 1576 Dihedral : 5.339 69.130 1262 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.22 % Allowed : 19.00 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1150 helix: 1.37 (0.26), residues: 406 sheet: -0.17 (0.29), residues: 285 loop : 0.03 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.007 0.001 HIS B 142 PHE 0.032 0.002 PHE H 68 TYR 0.016 0.002 TYR D 179 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 252 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 277 average time/residue: 1.1977 time to fit residues: 354.6617 Evaluate side-chains 261 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.3036 time to fit residues: 4.2022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.0060 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 304 ASN D 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9196 Z= 0.218 Angle : 0.547 6.883 12484 Z= 0.285 Chirality : 0.042 0.162 1437 Planarity : 0.004 0.049 1576 Dihedral : 5.175 70.116 1262 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.49 % Allowed : 20.77 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.58 (0.25), residues: 1150 helix: 1.42 (0.26), residues: 409 sheet: -0.25 (0.29), residues: 286 loop : 0.03 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS B 62 PHE 0.036 0.002 PHE H 68 TYR 0.016 0.002 TYR D 179 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 247 time to evaluate : 1.102 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 271 average time/residue: 1.1513 time to fit residues: 333.7161 Evaluate side-chains 264 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.2290 time to fit residues: 3.8400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 230 ASN D 44 GLN D 77 ASN D 304 ASN D 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9196 Z= 0.271 Angle : 0.566 9.251 12484 Z= 0.293 Chirality : 0.044 0.148 1437 Planarity : 0.004 0.062 1576 Dihedral : 5.202 70.543 1262 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.91 % Allowed : 20.46 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.49 (0.25), residues: 1150 helix: 1.44 (0.26), residues: 410 sheet: -0.31 (0.29), residues: 282 loop : -0.14 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.044 0.002 PHE H 68 TYR 0.025 0.002 TYR H 190 ARG 0.016 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 1.121 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 26 residues processed: 276 average time/residue: 1.2153 time to fit residues: 358.7675 Evaluate side-chains 268 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 13 residues processed: 13 average time/residue: 0.2244 time to fit residues: 5.3167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 230 ASN D 44 GLN D 59 ASN D 304 ASN D 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9196 Z= 0.211 Angle : 0.562 8.869 12484 Z= 0.287 Chirality : 0.042 0.148 1437 Planarity : 0.005 0.070 1576 Dihedral : 5.143 70.130 1262 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.18 % Allowed : 21.82 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.51 (0.25), residues: 1150 helix: 1.56 (0.26), residues: 409 sheet: -0.34 (0.29), residues: 272 loop : -0.20 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 62 PHE 0.035 0.002 PHE H 68 TYR 0.029 0.002 TYR H 190 ARG 0.017 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 252 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 23 residues processed: 275 average time/residue: 1.2078 time to fit residues: 355.0089 Evaluate side-chains 263 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 13 residues processed: 10 average time/residue: 0.1111 time to fit residues: 3.3427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 44 GLN D 59 ASN D 77 ASN D 304 ASN D 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9196 Z= 0.226 Angle : 0.568 10.467 12484 Z= 0.290 Chirality : 0.043 0.156 1437 Planarity : 0.004 0.047 1576 Dihedral : 5.123 69.686 1262 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.34 % Allowed : 23.28 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.50 (0.25), residues: 1150 helix: 1.54 (0.26), residues: 408 sheet: -0.30 (0.29), residues: 271 loop : -0.23 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS D 210 PHE 0.051 0.002 PHE A 55 TYR 0.032 0.002 TYR H 190 ARG 0.008 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 241 time to evaluate : 1.093 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 260 average time/residue: 1.3282 time to fit residues: 368.5426 Evaluate side-chains 258 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.1233 time to fit residues: 2.6136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 95 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 44 GLN D 77 ASN D 304 ASN D 374 ASN H 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9196 Z= 0.192 Angle : 0.563 10.812 12484 Z= 0.288 Chirality : 0.042 0.155 1437 Planarity : 0.005 0.049 1576 Dihedral : 5.141 69.975 1262 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.13 % Allowed : 24.43 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.50 (0.25), residues: 1150 helix: 1.52 (0.26), residues: 409 sheet: -0.35 (0.29), residues: 273 loop : -0.18 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS D 210 PHE 0.047 0.002 PHE A 55 TYR 0.028 0.001 TYR H 190 ARG 0.013 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 236 time to evaluate : 1.425 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 255 average time/residue: 1.2132 time to fit residues: 330.5159 Evaluate side-chains 248 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.0910 time to fit residues: 1.7585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 0.0060 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 44 GLN D 59 ASN D 304 ASN D 374 ASN H 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9196 Z= 0.181 Angle : 0.564 10.383 12484 Z= 0.286 Chirality : 0.042 0.187 1437 Planarity : 0.005 0.060 1576 Dihedral : 5.087 70.198 1262 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.61 % Allowed : 25.26 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.45 (0.25), residues: 1150 helix: 1.58 (0.26), residues: 408 sheet: -0.49 (0.28), residues: 290 loop : -0.22 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS B 62 PHE 0.049 0.002 PHE A 55 TYR 0.025 0.001 TYR H 190 ARG 0.014 0.001 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 1.135 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 255 average time/residue: 1.2148 time to fit residues: 332.0588 Evaluate side-chains 261 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.1659 time to fit residues: 1.8280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 89 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 230 ASN D 44 GLN D 59 ASN D 304 ASN D 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117589 restraints weight = 12097.966| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.84 r_work: 0.3389 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9196 Z= 0.195 Angle : 0.561 10.037 12484 Z= 0.286 Chirality : 0.042 0.154 1437 Planarity : 0.005 0.059 1576 Dihedral : 5.029 69.623 1262 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.61 % Allowed : 25.57 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.46 (0.25), residues: 1150 helix: 1.57 (0.26), residues: 408 sheet: -0.35 (0.29), residues: 278 loop : -0.29 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS D 210 PHE 0.046 0.002 PHE A 55 TYR 0.027 0.002 TYR H 190 ARG 0.014 0.001 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5192.64 seconds wall clock time: 92 minutes 43.67 seconds (5563.67 seconds total)