Starting phenix.real_space_refine on Sat Jul 4 08:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c1c_16378/07_2026/8c1c_16378.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.053 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 S 49 5.16 5 C 6226 2.51 5 N 1675 2.21 5 O 2033 1.98 5 H 9284 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19267 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6489 Classifications: {'peptide': 426} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 25, 'TRANS': 396} Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1624 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "R" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2685 Classifications: {'peptide': 171} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 163} Chain: "X" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6489 Classifications: {'peptide': 426} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 25, 'TRANS': 396} Chain: "Y" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1624 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY H 315 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY H 315 " occ=0.00 residue: pdb=" N HIS H 316 " occ=0.00 ... (15 atoms not shown) pdb=" HE2 HIS H 316 " occ=0.00 residue: pdb=" N GLY X 315 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY X 315 " occ=0.00 residue: pdb=" N HIS X 316 " occ=0.00 ... (15 atoms not shown) pdb=" HE2 HIS X 316 " occ=0.00 Time building chain proxies: 3.25, per 1000 atoms: 0.17 Number of scatterers: 19267 At special positions: 0 Unit cell: (116.06, 122.278, 138.857, 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) S 49 16.00 O 2033 8.00 N 1675 7.00 C 6226 6.00 H 9284 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 130 " - pdb=" SG CYS L 217 " distance=2.03 Simple disulfide: pdb=" SG CYS H 131 " - pdb=" SG CYS H 221 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS X 325 " distance=2.06 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 309 " distance=2.03 Simple disulfide: pdb=" SG CYS H 325 " - pdb=" SG CYS X 237 " distance=2.06 Simple disulfide: pdb=" SG CYS H 355 " - pdb=" SG CYS H 415 " distance=2.04 Simple disulfide: pdb=" SG CYS H 461 " - pdb=" SG CYS H 521 " distance=2.04 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 68 " distance=2.04 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 151 " distance=2.04 Simple disulfide: pdb=" SG CYS X 130 " - pdb=" SG CYS Y 217 " distance=2.03 Simple disulfide: pdb=" SG CYS X 131 " - pdb=" SG CYS X 221 " distance=2.03 Simple disulfide: pdb=" SG CYS X 145 " - pdb=" SG CYS X 201 " distance=2.03 Simple disulfide: pdb=" SG CYS X 251 " - pdb=" SG CYS X 309 " distance=2.04 Simple disulfide: pdb=" SG CYS X 355 " - pdb=" SG CYS X 415 " distance=2.04 Simple disulfide: pdb=" SG CYS X 461 " - pdb=" SG CYS X 521 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 137 " - pdb=" SG CYS Y 197 " distance=2.03 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 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " " MAN B 3 " - " MAN B 4 " " MAN C 3 " - " MAN C 4 " " BMA G 3 " - " MAN G 4 " ALPHA1-4 " NAG B 2 " - " MAN B 3 " " NAG C 2 " - " MAN C 3 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " " MAN B 3 " - " MAN B 5 " " MAN C 3 " - " MAN C 5 " " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 1 " - " ASN H 391 " " NAG B 1 " - " ASN R 166 " " NAG C 1 " - " ASN R 42 " " NAG D 1 " - " ASN R 21 " " NAG E 1 " - " ASN R 74 " " NAG F 1 " - " ASN R 135 " " NAG G 1 " - " ASN X 391 " " NAG R 201 " - " ASN R 50 " " NAG R 202 " - " ASN R 140 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 719.7 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 9.0% alpha, 50.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'H' and resid 273 through 275 No H-bonds generated for 'chain 'H' and resid 273 through 275' Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 403 through 409 Processing helix chain 'H' and resid 483 through 485 No H-bonds generated for 'chain 'H' and resid 483 through 485' Processing helix chain 'H' and resid 510 through 516 Processing helix chain 'L' and resid 124 through 131 Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'R' and resid 59 through 63 Processing helix chain 'R' and resid 111 through 113 No H-bonds generated for 'chain 'R' and resid 111 through 113' Processing helix chain 'R' and resid 142 through 146 removed outlier: 3.732A pdb=" N SER R 146 " --> pdb=" O VAL R 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 275 No H-bonds generated for 'chain 'X' and resid 273 through 275' Processing helix chain 'X' and resid 298 through 303 Processing helix chain 'X' and resid 341 through 347 Processing helix chain 'X' and resid 403 through 409 Processing helix chain 'X' and resid 483 through 485 No H-bonds generated for 'chain 'X' and resid 483 through 485' Processing helix chain 'X' and resid 510 through 516 Processing helix chain 'Y' and resid 124 through 131 Processing helix chain 'Y' and resid 186 through 192 removed outlier: 3.906A pdb=" N HIS Y 192 " --> pdb=" O ASP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 217 No H-bonds generated for 'chain 'Y' and resid 215 through 217' Processing sheet with id=AA1, first strand: chain 'H' and resid 123 through 128 Processing sheet with id=AA2, first strand: chain 'H' and resid 123 through 128 Processing sheet with id=AA3, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AA4, first strand: chain 'H' and resid 277 through 284 removed outlier: 6.433A pdb=" N ALA H 288 " --> pdb=" O GLY H 255 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY H 255 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN H 248 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLN X 248 " --> pdb=" O LEU X 296 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU X 296 " --> pdb=" O GLN X 248 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU X 250 " --> pdb=" O LEU X 294 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU X 294 " --> pdb=" O LEU X 250 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU X 252 " --> pdb=" O SER X 292 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N SER X 292 " --> pdb=" O LEU X 252 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER X 254 " --> pdb=" O THR X 290 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR X 290 " --> pdb=" O SER X 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'H' and resid 334 through 337 removed outlier: 4.434A pdb=" N ASP H 359 " --> pdb=" O LEU H 394 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU H 394 " --> pdb=" O ASP H 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 368 through 373 Processing sheet with id=AA8, first strand: chain 'H' and resid 441 through 446 removed outlier: 5.405A pdb=" N PHE H 500 " --> pdb=" O ASN H 465 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 441 through 446 removed outlier: 5.405A pdb=" N PHE H 500 " --> pdb=" O ASN H 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 480 through 481 Processing sheet with id=AB2, first strand: chain 'L' and resid 117 through 121 removed outlier: 5.135A pdb=" N SER L 134 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU L 184 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL L 136 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU L 182 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU L 138 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER L 180 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN L 140 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU L 178 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 148 through 153 Processing sheet with id=AB4, first strand: chain 'R' and resid 6 through 10 Processing sheet with id=AB5, first strand: chain 'R' and resid 15 through 17 removed outlier: 6.388A pdb=" N ILE R 16 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TRP R 39 " --> pdb=" O SER R 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 88 through 92 Processing sheet with id=AB7, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.962A pdb=" N VAL R 97 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR R 148 " --> pdb=" O LYS R 122 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS R 122 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR R 150 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR R 120 " --> pdb=" O TYR R 150 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR R 152 " --> pdb=" O VAL R 118 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL R 118 " --> pdb=" O THR R 152 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 128 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS R 122 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.962A pdb=" N VAL R 97 " --> pdb=" O ILE R 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 123 through 127 removed outlier: 5.327A pdb=" N THR X 142 " --> pdb=" O VAL X 190 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL X 190 " --> pdb=" O THR X 142 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY X 144 " --> pdb=" O LEU X 188 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU X 188 " --> pdb=" O GLY X 144 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU X 146 " --> pdb=" O SER X 186 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER X 186 " --> pdb=" O LEU X 146 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR X 148 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR X 184 " --> pdb=" O THR X 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 123 through 127 removed outlier: 5.327A pdb=" N THR X 142 " --> pdb=" O VAL X 190 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL X 190 " --> pdb=" O THR X 142 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY X 144 " --> pdb=" O LEU X 188 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU X 188 " --> pdb=" O GLY X 144 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU X 146 " --> pdb=" O SER X 186 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER X 186 " --> pdb=" O LEU X 146 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR X 148 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR X 184 " --> pdb=" O THR X 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 156 through 160 Processing sheet with id=AC3, first strand: chain 'X' and resid 270 through 271 Processing sheet with id=AC4, first strand: chain 'X' and resid 334 through 337 removed outlier: 3.740A pdb=" N ASP X 359 " --> pdb=" O LEU X 394 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU X 394 " --> pdb=" O ASP X 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 368 through 373 Processing sheet with id=AC6, first strand: chain 'X' and resid 441 through 446 removed outlier: 5.295A pdb=" N PHE X 500 " --> pdb=" O ASN X 465 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 441 through 446 removed outlier: 5.295A pdb=" N PHE X 500 " --> pdb=" O ASN X 465 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 480 through 481 Processing sheet with id=AC9, first strand: chain 'Y' and resid 117 through 121 removed outlier: 5.678A pdb=" N TYR Y 176 " --> pdb=" O ASN Y 141 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 157 through 158 removed outlier: 4.440A pdb=" N TRP Y 151 " --> pdb=" O GLN Y 158 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1137 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: 4.54 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9284 1.03 - 1.24: 1255 1.24 - 1.44: 3240 1.44 - 1.65: 5663 1.65 - 1.85: 62 Bond restraints: 19504 Sorted by residual: bond pdb=" CB TRP R 13 " pdb=" CG TRP R 13 " ideal model delta sigma weight residual 1.498 1.612 -0.114 3.10e-02 1.04e+03 1.36e+01 bond pdb=" CB LYS R 122 " pdb=" CG LYS R 122 " ideal model delta sigma weight residual 1.520 1.600 -0.080 3.00e-02 1.11e+03 7.10e+00 bond pdb=" C LYS R 4 " pdb=" N PRO R 5 " ideal model delta sigma weight residual 1.335 1.358 -0.023 8.70e-03 1.32e+04 7.00e+00 bond pdb=" CA VAL R 22 " pdb=" CB VAL R 22 " ideal model delta sigma weight residual 1.540 1.570 -0.030 1.36e-02 5.41e+03 4.71e+00 bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.67e+00 ... (remaining 19499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 33247 2.28 - 4.57: 1504 4.57 - 6.85: 235 6.85 - 9.14: 26 9.14 - 11.42: 7 Bond angle restraints: 35019 Sorted by residual: angle pdb=" CA GLN R 157 " pdb=" CB GLN R 157 " pdb=" CG GLN R 157 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 angle pdb=" C GLU H 319 " pdb=" CA GLU H 319 " pdb=" CB GLU H 319 " ideal model delta sigma weight residual 110.62 102.00 8.62 1.86e+00 2.89e-01 2.15e+01 angle pdb=" C ASN H 391 " pdb=" CA ASN H 391 " pdb=" CB ASN H 391 " ideal model delta sigma weight residual 110.57 118.97 -8.40 1.93e+00 2.68e-01 1.89e+01 angle pdb=" N PRO X 228 " pdb=" CA PRO X 228 " pdb=" C PRO X 228 " ideal model delta sigma weight residual 111.38 104.64 6.74 1.59e+00 3.96e-01 1.80e+01 angle pdb=" N ASN R 135 " pdb=" CA ASN R 135 " pdb=" C ASN R 135 " ideal model delta sigma weight residual 107.49 98.84 8.65 2.16e+00 2.14e-01 1.61e+01 ... (remaining 35014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8347 17.84 - 35.68: 648 35.68 - 53.52: 164 53.52 - 71.36: 41 71.36 - 89.20: 14 Dihedral angle restraints: 9214 sinusoidal: 4983 harmonic: 4231 Sorted by residual: dihedral pdb=" CB CYS H 237 " pdb=" SG CYS H 237 " pdb=" SG CYS X 325 " pdb=" CB CYS X 325 " ideal model delta sinusoidal sigma weight residual -86.00 -173.89 87.89 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS R 26 " pdb=" SG CYS R 26 " pdb=" SG CYS R 68 " pdb=" CB CYS R 68 " ideal model delta sinusoidal sigma weight residual 93.00 21.02 71.98 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS H 325 " pdb=" SG CYS H 325 " pdb=" SG CYS X 237 " pdb=" CB CYS X 237 " ideal model delta sinusoidal sigma weight residual 93.00 162.85 -69.85 1 1.00e+01 1.00e-02 6.29e+01 ... (remaining 9211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1251 0.063 - 0.127: 331 0.127 - 0.190: 68 0.190 - 0.254: 16 0.254 - 0.317: 5 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA GLN R 157 " pdb=" N GLN R 157 " pdb=" C GLN R 157 " pdb=" CB GLN R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C1 NAG R 201 " pdb=" ND2 ASN R 50 " pdb=" C2 NAG R 201 " pdb=" O5 NAG R 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA VAL R 22 " pdb=" N VAL R 22 " pdb=" C VAL R 22 " pdb=" CB VAL R 22 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1668 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 74 " -0.003 2.00e-02 2.50e+03 5.00e-02 3.13e+01 pdb=" CG ASN R 74 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN R 74 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN R 74 " 0.075 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 156 " -0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" C TRP R 156 " 0.090 2.00e-02 2.50e+03 pdb=" O TRP R 156 " -0.034 2.00e-02 2.50e+03 pdb=" N GLN R 157 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 391 " 0.046 2.00e-02 2.50e+03 4.23e-02 2.24e+01 pdb=" CG ASN H 391 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN H 391 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN H 391 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " 0.041 2.00e-02 2.50e+03 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 3628 2.29 - 2.87: 41280 2.87 - 3.45: 46342 3.45 - 4.02: 67002 4.02 - 4.60: 98016 Nonbonded interactions: 256268 Sorted by model distance: nonbonded pdb="HE21 GLN R 69 " pdb=" O HIS R 70 " model vdw 1.715 2.450 nonbonded pdb=" H LEU X 176 " pdb=" O HIS X 181 " model vdw 1.732 2.450 nonbonded pdb=" O TYR L 189 " pdb=" HH TYR L 195 " model vdw 1.735 2.450 nonbonded pdb=" HZ1 LYS R 67 " pdb=" O SER R 76 " model vdw 1.745 2.450 nonbonded pdb=" HZ3 LYS H 216 " pdb=" OE2 GLU L 126 " model vdw 1.753 2.450 ... (remaining 256263 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' and (resid 1 through 2 or resid 4 through 5)) selection = (chain 'B' and (resid 1 through 2 or resid 4 through 5)) selection = (chain 'C' and (resid 1 through 2 or resid 4 through 5)) selection = (chain 'G' and (resid 1 through 2 or resid 4 through 5)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'Y' } 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=0.00 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: 4.440 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: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.970 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.008 0.114 10266 Z= 0.336 Angle : 1.299 25.148 14058 Z= 0.658 Chirality : 0.064 0.317 1671 Planarity : 0.008 0.096 1746 Dihedral : 13.165 89.203 3566 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1227 helix: -2.07 (0.44), residues: 87 sheet: 0.71 (0.22), residues: 575 loop : -0.71 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 15 TYR 0.047 0.003 TYR R 149 PHE 0.050 0.004 PHE R 17 TRP 0.054 0.004 TRP R 13 HIS 0.023 0.003 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.33 (10220) covalent geometry : angle 1.21214 / 0.64 (13938) SS BOND : bond 0.01041 / 0.66 ( 18) SS BOND : angle 4.28482 / 2.64 ( 36) hydrogen bonds : bond 0.09507 / 6.35 ( 382) hydrogen bonds : angle 6.50635 / 4.59 ( 1137) link_ALPHA1-3 : bond 0.00586 / 0.27 ( 4) link_ALPHA1-3 : angle 1.79926 / 1.02 ( 12) link_ALPHA1-4 : bond 0.01262 / 0.60 ( 2) link_ALPHA1-4 : angle 2.38053 / 1.45 ( 6) link_ALPHA1-6 : bond 0.00771 / 0.29 ( 4) link_ALPHA1-6 : angle 1.38886 / 0.81 ( 12) link_BETA1-4 : bond 0.01208 / 0.86 ( 9) link_BETA1-4 : angle 2.86967 / 1.99 ( 27) link_NAG-ASN : bond 0.01433 / 1.04 ( 9) link_NAG-ASN : angle 9.19204 / 5.41 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.3094 time to fit residues: 12.4335 Evaluate side-chains 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 140 ASN X 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.058431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.043146 restraints weight = 295525.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.045220 restraints weight = 116579.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.046338 restraints weight = 61229.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.046975 restraints weight = 40720.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.047202 restraints weight = 32044.410| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10266 Z= 0.138 Angle : 0.659 16.078 14058 Z= 0.319 Chirality : 0.043 0.290 1671 Planarity : 0.005 0.048 1746 Dihedral : 5.915 79.336 1327 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1227 helix: -1.75 (0.47), residues: 87 sheet: 0.96 (0.21), residues: 587 loop : -0.15 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 348 TYR 0.012 0.001 TYR X 307 PHE 0.010 0.001 PHE H 151 TRP 0.028 0.001 TRP X 513 HIS 0.008 0.001 HIS R 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (10220) covalent geometry : angle 0.60396 / 0.31 (13938) SS BOND : bond 0.00375 / 0.23 ( 18) SS BOND : angle 1.36378 / 0.93 ( 36) hydrogen bonds : bond 0.03645 / 2.47 ( 382) hydrogen bonds : angle 5.46377 / 3.82 ( 1137) link_ALPHA1-3 : bond 0.00695 / 0.31 ( 4) link_ALPHA1-3 : angle 1.76335 / 1.06 ( 12) link_ALPHA1-4 : bond 0.01193 / 0.57 ( 2) link_ALPHA1-4 : angle 2.24686 / 1.33 ( 6) link_ALPHA1-6 : bond 0.00787 / 0.32 ( 4) link_ALPHA1-6 : angle 1.60741 / 0.97 ( 12) link_BETA1-4 : bond 0.00415 / 0.27 ( 9) link_BETA1-4 : angle 1.82421 / 1.16 ( 27) link_NAG-ASN : bond 0.00729 / 0.54 ( 9) link_NAG-ASN : angle 5.34023 / 3.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.2533 time to fit residues: 9.3426 Evaluate side-chains 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.056931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.041713 restraints weight = 310653.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.043653 restraints weight = 123651.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.044696 restraints weight = 66195.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.045174 restraints weight = 44927.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.045526 restraints weight = 36609.179| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10266 Z= 0.182 Angle : 0.651 12.508 14058 Z= 0.311 Chirality : 0.042 0.309 1671 Planarity : 0.005 0.104 1746 Dihedral : 5.498 72.891 1327 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1227 helix: -1.71 (0.44), residues: 89 sheet: 0.94 (0.21), residues: 582 loop : -0.16 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 106 TYR 0.017 0.002 TYR R 120 PHE 0.011 0.001 PHE R 17 TRP 0.021 0.002 TRP X 513 HIS 0.014 0.001 HIS R 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (10220) covalent geometry : angle 0.60940 / 0.30 (13938) SS BOND : bond 0.00899 / 0.53 ( 18) SS BOND : angle 1.63381 / 1.06 ( 36) hydrogen bonds : bond 0.03152 / 2.15 ( 382) hydrogen bonds : angle 5.18419 / 3.61 ( 1137) link_ALPHA1-3 : bond 0.00911 / 0.39 ( 4) link_ALPHA1-3 : angle 1.75676 / 1.03 ( 12) link_ALPHA1-4 : bond 0.00887 / 0.42 ( 2) link_ALPHA1-4 : angle 2.58434 / 1.53 ( 6) link_ALPHA1-6 : bond 0.00772 / 0.30 ( 4) link_ALPHA1-6 : angle 1.54312 / 0.92 ( 12) link_BETA1-4 : bond 0.00538 / 0.34 ( 9) link_BETA1-4 : angle 2.02708 / 1.24 ( 27) link_NAG-ASN : bond 0.00592 / 0.40 ( 9) link_NAG-ASN : angle 4.16965 / 2.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2119 time to fit residues: 6.8756 Evaluate side-chains 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.057226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.041991 restraints weight = 310657.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.043948 restraints weight = 121576.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.045011 restraints weight = 64945.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.045500 restraints weight = 44066.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.045688 restraints weight = 36003.801| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10266 Z= 0.116 Angle : 0.582 15.024 14058 Z= 0.277 Chirality : 0.043 0.432 1671 Planarity : 0.004 0.048 1746 Dihedral : 5.251 72.574 1327 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.24), residues: 1227 helix: -1.38 (0.48), residues: 89 sheet: 0.97 (0.21), residues: 581 loop : -0.01 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 424 TYR 0.010 0.001 TYR X 307 PHE 0.010 0.001 PHE X 501 TRP 0.017 0.001 TRP X 513 HIS 0.006 0.001 HIS R 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10220) covalent geometry : angle 0.53812 / 0.27 (13938) SS BOND : bond 0.00291 / 0.16 ( 18) SS BOND : angle 1.43931 / 0.85 ( 36) hydrogen bonds : bond 0.02776 / 1.89 ( 382) hydrogen bonds : angle 4.97971 / 3.46 ( 1137) link_ALPHA1-3 : bond 0.00557 / 0.26 ( 4) link_ALPHA1-3 : angle 1.64655 / 0.98 ( 12) link_ALPHA1-4 : bond 0.00944 / 0.45 ( 2) link_ALPHA1-4 : angle 2.10914 / 1.23 ( 6) link_ALPHA1-6 : bond 0.00605 / 0.24 ( 4) link_ALPHA1-6 : angle 1.46214 / 0.89 ( 12) link_BETA1-4 : bond 0.00393 / 0.27 ( 9) link_BETA1-4 : angle 1.42350 / 0.88 ( 27) link_NAG-ASN : bond 0.00553 / 0.41 ( 9) link_NAG-ASN : angle 4.37759 / 2.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 GLU cc_start: 0.4799 (tp30) cc_final: 0.4533 (mm-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2541 time to fit residues: 8.0689 Evaluate side-chains 21 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 118 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 298 GLN ** H 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.055533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.040222 restraints weight = 306295.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.042060 restraints weight = 122268.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.043013 restraints weight = 66107.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.043554 restraints weight = 45669.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.043814 restraints weight = 36651.154| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10266 Z= 0.243 Angle : 0.695 14.771 14058 Z= 0.330 Chirality : 0.042 0.430 1671 Planarity : 0.004 0.045 1746 Dihedral : 5.361 68.914 1327 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1227 helix: -1.47 (0.46), residues: 89 sheet: 0.66 (0.21), residues: 585 loop : -0.24 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 331 TYR 0.016 0.002 TYR X 307 PHE 0.012 0.001 PHE H 445 TRP 0.017 0.002 TRP X 513 HIS 0.015 0.002 HIS R 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 (10220) covalent geometry : angle 0.63665 / 0.32 (13938) SS BOND : bond 0.00636 / 0.36 ( 18) SS BOND : angle 2.02479 / 1.24 ( 36) hydrogen bonds : bond 0.03256 / 2.21 ( 382) hydrogen bonds : angle 5.18468 / 3.59 ( 1137) link_ALPHA1-3 : bond 0.00748 / 0.31 ( 4) link_ALPHA1-3 : angle 1.77478 / 1.02 ( 12) link_ALPHA1-4 : bond 0.00801 / 0.38 ( 2) link_ALPHA1-4 : angle 2.91364 / 1.74 ( 6) link_ALPHA1-6 : bond 0.00605 / 0.23 ( 4) link_ALPHA1-6 : angle 1.59050 / 0.93 ( 12) link_BETA1-4 : bond 0.00603 / 0.34 ( 9) link_BETA1-4 : angle 2.32945 / 1.32 ( 27) link_NAG-ASN : bond 0.01063 / 0.74 ( 9) link_NAG-ASN : angle 5.20486 / 3.20 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2043 time to fit residues: 6.3184 Evaluate side-chains 18 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.056026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.040812 restraints weight = 306322.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.042681 restraints weight = 120785.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.043711 restraints weight = 65273.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.044192 restraints weight = 44312.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.044391 restraints weight = 35998.745| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10266 Z= 0.142 Angle : 0.584 10.489 14058 Z= 0.280 Chirality : 0.041 0.327 1671 Planarity : 0.004 0.049 1746 Dihedral : 5.182 70.073 1327 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1227 helix: -1.36 (0.47), residues: 89 sheet: 0.67 (0.21), residues: 587 loop : -0.08 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 106 TYR 0.012 0.001 TYR X 307 PHE 0.011 0.001 PHE X 501 TRP 0.016 0.001 TRP X 513 HIS 0.007 0.001 HIS R 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (10220) covalent geometry : angle 0.54669 / 0.27 (13938) SS BOND : bond 0.00286 / 0.17 ( 18) SS BOND : angle 1.41753 / 0.89 ( 36) hydrogen bonds : bond 0.02819 / 1.93 ( 382) hydrogen bonds : angle 4.99502 / 3.46 ( 1137) link_ALPHA1-3 : bond 0.00597 / 0.27 ( 4) link_ALPHA1-3 : angle 1.64170 / 0.96 ( 12) link_ALPHA1-4 : bond 0.00949 / 0.45 ( 2) link_ALPHA1-4 : angle 2.16719 / 1.28 ( 6) link_ALPHA1-6 : bond 0.00661 / 0.25 ( 4) link_ALPHA1-6 : angle 1.51355 / 0.91 ( 12) link_BETA1-4 : bond 0.00539 / 0.39 ( 9) link_BETA1-4 : angle 1.51696 / 0.92 ( 27) link_NAG-ASN : bond 0.00526 / 0.37 ( 9) link_NAG-ASN : angle 3.86700 / 2.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2505 time to fit residues: 7.8418 Evaluate side-chains 19 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.056382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.041068 restraints weight = 303615.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.042987 restraints weight = 118726.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.044040 restraints weight = 63952.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.044585 restraints weight = 43270.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.044783 restraints weight = 34649.910| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10266 Z= 0.101 Angle : 0.550 10.020 14058 Z= 0.267 Chirality : 0.041 0.263 1671 Planarity : 0.004 0.048 1746 Dihedral : 5.033 71.258 1327 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1227 helix: -1.20 (0.49), residues: 89 sheet: 0.80 (0.21), residues: 583 loop : 0.01 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 106 TYR 0.010 0.001 TYR R 120 PHE 0.010 0.001 PHE X 501 TRP 0.046 0.001 TRP X 513 HIS 0.004 0.001 HIS X 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (10220) covalent geometry : angle 0.51895 / 0.26 (13938) SS BOND : bond 0.00221 / 0.13 ( 18) SS BOND : angle 1.73546 / 0.96 ( 36) hydrogen bonds : bond 0.02620 / 1.79 ( 382) hydrogen bonds : angle 4.80723 / 3.34 ( 1137) link_ALPHA1-3 : bond 0.00529 / 0.25 ( 4) link_ALPHA1-3 : angle 1.63016 / 0.96 ( 12) link_ALPHA1-4 : bond 0.00925 / 0.44 ( 2) link_ALPHA1-4 : angle 1.82071 / 1.07 ( 6) link_ALPHA1-6 : bond 0.00599 / 0.24 ( 4) link_ALPHA1-6 : angle 1.42012 / 0.89 ( 12) link_BETA1-4 : bond 0.00408 / 0.28 ( 9) link_BETA1-4 : angle 1.42706 / 0.88 ( 27) link_NAG-ASN : bond 0.00414 / 0.31 ( 9) link_NAG-ASN : angle 3.13752 / 1.98 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2647 time to fit residues: 7.4445 Evaluate side-chains 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 30.0000 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.056345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.040996 restraints weight = 317195.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.042962 restraints weight = 124639.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.044008 restraints weight = 66980.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.044557 restraints weight = 45842.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.044753 restraints weight = 36986.403| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10266 Z= 0.108 Angle : 0.572 12.549 14058 Z= 0.272 Chirality : 0.041 0.257 1671 Planarity : 0.004 0.048 1746 Dihedral : 4.998 71.864 1327 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1227 helix: -1.05 (0.50), residues: 89 sheet: 0.82 (0.21), residues: 577 loop : 0.04 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 331 TYR 0.009 0.001 TYR X 307 PHE 0.015 0.001 PHE H 151 TRP 0.031 0.001 TRP X 513 HIS 0.024 0.001 HIS H 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10220) covalent geometry : angle 0.52369 / 0.26 (13938) SS BOND : bond 0.00239 / 0.13 ( 18) SS BOND : angle 1.78205 / 1.21 ( 36) hydrogen bonds : bond 0.02553 / 1.73 ( 382) hydrogen bonds : angle 4.73712 / 3.29 ( 1137) link_ALPHA1-3 : bond 0.00526 / 0.25 ( 4) link_ALPHA1-3 : angle 1.58806 / 0.93 ( 12) link_ALPHA1-4 : bond 0.00838 / 0.40 ( 2) link_ALPHA1-4 : angle 1.87132 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00577 / 0.23 ( 4) link_ALPHA1-6 : angle 1.42635 / 0.89 ( 12) link_BETA1-4 : bond 0.00396 / 0.27 ( 9) link_BETA1-4 : angle 1.53849 / 0.94 ( 27) link_NAG-ASN : bond 0.00506 / 0.37 ( 9) link_NAG-ASN : angle 4.39128 / 2.66 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2739 time to fit residues: 8.1841 Evaluate side-chains 19 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 118 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.056564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.041261 restraints weight = 311669.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.043232 restraints weight = 121170.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.044289 restraints weight = 65052.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.044798 restraints weight = 44281.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.044988 restraints weight = 36245.246| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10266 Z= 0.090 Angle : 0.543 11.424 14058 Z= 0.259 Chirality : 0.041 0.279 1671 Planarity : 0.004 0.045 1746 Dihedral : 4.870 73.378 1327 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.24), residues: 1227 helix: -0.81 (0.52), residues: 87 sheet: 0.79 (0.21), residues: 589 loop : 0.10 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 331 TYR 0.008 0.001 TYR R 120 PHE 0.012 0.001 PHE H 151 TRP 0.030 0.001 TRP X 513 HIS 0.006 0.001 HIS H 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (10220) covalent geometry : angle 0.50490 / 0.25 (13938) SS BOND : bond 0.00216 / 0.14 ( 18) SS BOND : angle 1.34785 / 0.90 ( 36) hydrogen bonds : bond 0.02462 / 1.66 ( 382) hydrogen bonds : angle 4.60921 / 3.20 ( 1137) link_ALPHA1-3 : bond 0.00485 / 0.23 ( 4) link_ALPHA1-3 : angle 1.56862 / 0.93 ( 12) link_ALPHA1-4 : bond 0.00834 / 0.40 ( 2) link_ALPHA1-4 : angle 1.66665 / 0.97 ( 6) link_ALPHA1-6 : bond 0.00565 / 0.23 ( 4) link_ALPHA1-6 : angle 1.40004 / 0.88 ( 12) link_BETA1-4 : bond 0.00507 / 0.35 ( 9) link_BETA1-4 : angle 1.36717 / 0.84 ( 27) link_NAG-ASN : bond 0.00344 / 0.26 ( 9) link_NAG-ASN : angle 3.91026 / 2.38 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2734 time to fit residues: 8.1700 Evaluate side-chains 19 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.056289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.041044 restraints weight = 311901.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.042994 restraints weight = 122988.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.044044 restraints weight = 65821.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.044543 restraints weight = 44621.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.044855 restraints weight = 36565.777| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10266 Z= 0.098 Angle : 0.532 9.603 14058 Z= 0.254 Chirality : 0.040 0.248 1671 Planarity : 0.004 0.046 1746 Dihedral : 4.790 73.816 1327 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1227 helix: -0.67 (0.53), residues: 86 sheet: 0.78 (0.21), residues: 591 loop : 0.13 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 331 TYR 0.008 0.001 TYR X 307 PHE 0.010 0.001 PHE H 151 TRP 0.027 0.001 TRP X 513 HIS 0.007 0.001 HIS H 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10220) covalent geometry : angle 0.49853 / 0.25 (13938) SS BOND : bond 0.00181 / 0.11 ( 18) SS BOND : angle 1.20411 / 0.79 ( 36) hydrogen bonds : bond 0.02430 / 1.63 ( 382) hydrogen bonds : angle 4.54037 / 3.14 ( 1137) link_ALPHA1-3 : bond 0.00483 / 0.23 ( 4) link_ALPHA1-3 : angle 1.57121 / 0.93 ( 12) link_ALPHA1-4 : bond 0.00756 / 0.36 ( 2) link_ALPHA1-4 : angle 1.72969 / 1.01 ( 6) link_ALPHA1-6 : bond 0.00544 / 0.22 ( 4) link_ALPHA1-6 : angle 1.42483 / 0.90 ( 12) link_BETA1-4 : bond 0.00429 / 0.28 ( 9) link_BETA1-4 : angle 1.51197 / 0.91 ( 27) link_NAG-ASN : bond 0.00365 / 0.27 ( 9) link_NAG-ASN : angle 3.45878 / 2.14 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 GLU cc_start: 0.5161 (tp30) cc_final: 0.4943 (mm-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2530 time to fit residues: 8.1538 Evaluate side-chains 19 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 16 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 HIS ** H 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN ** R 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 389 GLN ** X 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.053958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.038698 restraints weight = 318857.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.040437 restraints weight = 128494.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.041421 restraints weight = 71027.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.041923 restraints weight = 49064.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.042119 restraints weight = 40196.349| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 10266 Z= 0.319 Angle : 0.781 13.666 14058 Z= 0.379 Chirality : 0.043 0.230 1671 Planarity : 0.005 0.050 1746 Dihedral : 5.484 71.354 1327 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1227 helix: -1.04 (0.49), residues: 88 sheet: 0.21 (0.21), residues: 568 loop : -0.32 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 331 TYR 0.022 0.002 TYR H 336 PHE 0.042 0.002 PHE R 17 TRP 0.029 0.003 TRP R 13 HIS 0.014 0.003 HIS X 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.32 (10220) covalent geometry : angle 0.72981 / 0.37 (13938) SS BOND : bond 0.00370 / 0.23 ( 18) SS BOND : angle 1.63609 / 1.10 ( 36) hydrogen bonds : bond 0.03858 / 2.61 ( 382) hydrogen bonds : angle 5.27350 / 3.66 ( 1137) link_ALPHA1-3 : bond 0.00661 / 0.28 ( 4) link_ALPHA1-3 : angle 1.78674 / 1.05 ( 12) link_ALPHA1-4 : bond 0.00970 / 0.46 ( 2) link_ALPHA1-4 : angle 3.76747 / 2.25 ( 6) link_ALPHA1-6 : bond 0.00638 / 0.23 ( 4) link_ALPHA1-6 : angle 1.76392 / 1.03 ( 12) link_BETA1-4 : bond 0.01051 / 0.62 ( 9) link_BETA1-4 : angle 2.89242 / 1.60 ( 27) link_NAG-ASN : bond 0.00898 / 0.59 ( 9) link_NAG-ASN : angle 4.95014 / 3.06 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4568.53 seconds wall clock time: 78 minutes 22.10 seconds (4702.10 seconds total)