Starting phenix.real_space_refine on Sun Aug 24 11:58:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1c_16378/08_2025/8c1c_16378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1c_16378/08_2025/8c1c_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c1c_16378/08_2025/8c1c_16378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1c_16378/08_2025/8c1c_16378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c1c_16378/08_2025/8c1c_16378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1c_16378/08_2025/8c1c_16378.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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: 3.15, per 1000 atoms: 0.16 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: 1.51 Conformation dependent library (CDL) restraints added in 612.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 4.52 Time building geometry restraints manager: 1.97 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 - 24.46: 9205 24.46 - 48.91: 459 48.91 - 73.37: 80 73.37 - 97.83: 24 97.83 - 122.28: 10 Dihedral angle restraints: 9778 sinusoidal: 5547 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 9775 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: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 14.929 122.285 4130 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 aren 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 covalent geometry : bond 0.00761 (10220) covalent geometry : angle 1.21214 (13938) SS BOND : bond 0.01041 ( 18) SS BOND : angle 4.28482 ( 36) hydrogen bonds : bond 0.09507 ( 382) hydrogen bonds : angle 6.50635 ( 1137) link_ALPHA1-3 : bond 0.00586 ( 4) link_ALPHA1-3 : angle 1.79926 ( 12) link_ALPHA1-4 : bond 0.01262 ( 2) link_ALPHA1-4 : angle 2.38053 ( 6) link_ALPHA1-6 : bond 0.00771 ( 4) link_ALPHA1-6 : angle 1.38886 ( 12) link_BETA1-4 : bond 0.01208 ( 9) link_BETA1-4 : angle 2.86967 ( 27) link_NAG-ASN : bond 0.01433 ( 9) link_NAG-ASN : angle 9.19204 ( 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 : 0.431 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: 0.2609 time to fit residues: 10.3820 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 : 0.520 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: X 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.058432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.043203 restraints weight = 295683.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.045271 restraints weight = 117249.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.046349 restraints weight = 62498.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.046935 restraints weight = 41398.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.047162 restraints weight = 33077.235| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10266 Z= 0.142 Angle : 0.667 18.307 14058 Z= 0.321 Chirality : 0.044 0.368 1671 Planarity : 0.005 0.049 1746 Dihedral : 10.847 110.902 1891 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.92 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 aren not related in a simple way. whole: 0.34 (0.24), residues: 1227 helix: -1.76 (0.47), residues: 88 sheet: 0.96 (0.21), residues: 587 loop : -0.15 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 348 TYR 0.012 0.001 TYR R 120 PHE 0.010 0.001 PHE H 151 TRP 0.030 0.001 TRP X 513 HIS 0.008 0.001 HIS R 134 Details of bonding type rmsd covalent geometry : bond 0.00295 (10220) covalent geometry : angle 0.60583 (13938) SS BOND : bond 0.00334 ( 18) SS BOND : angle 1.26452 ( 36) hydrogen bonds : bond 0.03585 ( 382) hydrogen bonds : angle 5.45293 ( 1137) link_ALPHA1-3 : bond 0.00816 ( 4) link_ALPHA1-3 : angle 2.36265 ( 12) link_ALPHA1-4 : bond 0.01576 ( 2) link_ALPHA1-4 : angle 2.68778 ( 6) link_ALPHA1-6 : bond 0.00862 ( 4) link_ALPHA1-6 : angle 1.75056 ( 12) link_BETA1-4 : bond 0.00461 ( 9) link_BETA1-4 : angle 1.90815 ( 27) link_NAG-ASN : bond 0.00570 ( 9) link_NAG-ASN : angle 5.56640 ( 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 : 0.348 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: 0.2234 time to fit residues: 8.2212 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 : 0.530 ------------------------------------------------------------------------------- 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: 0.7980 chunk 84 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4129 r_free = 0.4129 target = 0.056748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.041481 restraints weight = 305707.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.043411 restraints weight = 121468.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.044412 restraints weight = 65090.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.045020 restraints weight = 44499.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 76)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.045278 restraints weight = 35788.575| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10266 Z= 0.194 Angle : 0.679 14.763 14058 Z= 0.323 Chirality : 0.044 0.327 1671 Planarity : 0.005 0.092 1746 Dihedral : 9.693 111.011 1891 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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 aren not related in a simple way. whole: 0.32 (0.24), residues: 1227 helix: -1.70 (0.44), residues: 89 sheet: 0.93 (0.21), residues: 582 loop : -0.15 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 331 TYR 0.017 0.002 TYR H 182 PHE 0.011 0.001 PHE H 445 TRP 0.020 0.002 TRP X 513 HIS 0.015 0.001 HIS R 41 Details of bonding type rmsd covalent geometry : bond 0.00394 (10220) covalent geometry : angle 0.63191 (13938) SS BOND : bond 0.00822 ( 18) SS BOND : angle 1.97112 ( 36) hydrogen bonds : bond 0.03246 ( 382) hydrogen bonds : angle 5.21806 ( 1137) link_ALPHA1-3 : bond 0.00962 ( 4) link_ALPHA1-3 : angle 2.05613 ( 12) link_ALPHA1-4 : bond 0.01174 ( 2) link_ALPHA1-4 : angle 2.95586 ( 6) link_ALPHA1-6 : bond 0.00736 ( 4) link_ALPHA1-6 : angle 2.00297 ( 12) link_BETA1-4 : bond 0.00526 ( 9) link_BETA1-4 : angle 2.12632 ( 27) link_NAG-ASN : bond 0.00591 ( 9) link_NAG-ASN : angle 4.31385 ( 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 : 0.429 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: 0.2487 time to fit residues: 7.7573 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 : 0.372 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 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: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.056505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.041232 restraints weight = 312423.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.043167 restraints weight = 122704.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.044159 restraints weight = 65863.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.044752 restraints weight = 45230.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.044999 restraints weight = 36472.066| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10266 Z= 0.169 Angle : 0.626 11.914 14058 Z= 0.299 Chirality : 0.043 0.434 1671 Planarity : 0.004 0.047 1746 Dihedral : 8.765 108.675 1891 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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 aren not related in a simple way. whole: 0.28 (0.24), residues: 1227 helix: -1.50 (0.47), residues: 89 sheet: 0.81 (0.21), residues: 589 loop : -0.12 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 331 TYR 0.013 0.001 TYR X 307 PHE 0.011 0.001 PHE X 501 TRP 0.019 0.001 TRP X 513 HIS 0.010 0.001 HIS R 41 Details of bonding type rmsd covalent geometry : bond 0.00346 (10220) covalent geometry : angle 0.57975 (13938) SS BOND : bond 0.00934 ( 18) SS BOND : angle 1.82691 ( 36) hydrogen bonds : bond 0.02966 ( 382) hydrogen bonds : angle 5.07210 ( 1137) link_ALPHA1-3 : bond 0.00956 ( 4) link_ALPHA1-3 : angle 2.22503 ( 12) link_ALPHA1-4 : bond 0.01340 ( 2) link_ALPHA1-4 : angle 3.02407 ( 6) link_ALPHA1-6 : bond 0.00772 ( 4) link_ALPHA1-6 : angle 1.57795 ( 12) link_BETA1-4 : bond 0.00431 ( 9) link_BETA1-4 : angle 1.67868 ( 27) link_NAG-ASN : bond 0.00766 ( 9) link_NAG-ASN : angle 4.26283 ( 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 21 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.376 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: 0.2717 time to fit residues: 8.0744 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 : 0.533 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 37 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 389 GLN ** 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 = 0.4072 r_free = 0.4072 target = 0.055098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.039769 restraints weight = 311394.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.041587 restraints weight = 125341.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.042608 restraints weight = 68268.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.043142 restraints weight = 46569.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.043415 restraints weight = 37797.679| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10266 Z= 0.241 Angle : 0.699 14.963 14058 Z= 0.336 Chirality : 0.043 0.359 1671 Planarity : 0.005 0.049 1746 Dihedral : 8.732 110.315 1891 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 aren not related in a simple way. whole: -0.10 (0.24), residues: 1227 helix: -1.49 (0.46), residues: 89 sheet: 0.51 (0.21), residues: 582 loop : -0.34 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 331 TYR 0.027 0.002 TYR R 80 PHE 0.012 0.002 PHE H 445 TRP 0.017 0.002 TRP X 513 HIS 0.015 0.002 HIS R 41 Details of bonding type rmsd covalent geometry : bond 0.00487 (10220) covalent geometry : angle 0.64660 (13938) SS BOND : bond 0.00486 ( 18) SS BOND : angle 1.79510 ( 36) hydrogen bonds : bond 0.03279 ( 382) hydrogen bonds : angle 5.22937 ( 1137) link_ALPHA1-3 : bond 0.00975 ( 4) link_ALPHA1-3 : angle 2.05783 ( 12) link_ALPHA1-4 : bond 0.00828 ( 2) link_ALPHA1-4 : angle 2.82020 ( 6) link_ALPHA1-6 : bond 0.00688 ( 4) link_ALPHA1-6 : angle 1.62477 ( 12) link_BETA1-4 : bond 0.00699 ( 9) link_BETA1-4 : angle 2.03152 ( 27) link_NAG-ASN : bond 0.01005 ( 9) link_NAG-ASN : angle 5.02900 ( 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 : 0.540 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1764 time to fit residues: 5.5368 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 : 0.365 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.055811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.040527 restraints weight = 313951.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.042386 restraints weight = 124711.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.043402 restraints weight = 67231.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.043902 restraints weight = 45829.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.044188 restraints weight = 37502.639| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10266 Z= 0.138 Angle : 0.593 9.789 14058 Z= 0.287 Chirality : 0.042 0.334 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.317 108.848 1891 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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 aren not related in a simple way. whole: 0.08 (0.24), residues: 1227 helix: -1.43 (0.48), residues: 89 sheet: 0.59 (0.21), residues: 577 loop : -0.15 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 106 TYR 0.012 0.001 TYR R 80 PHE 0.011 0.001 PHE X 501 TRP 0.044 0.001 TRP X 513 HIS 0.006 0.001 HIS R 41 Details of bonding type rmsd covalent geometry : bond 0.00289 (10220) covalent geometry : angle 0.55364 (13938) SS BOND : bond 0.00334 ( 18) SS BOND : angle 1.88557 ( 36) hydrogen bonds : bond 0.02882 ( 382) hydrogen bonds : angle 5.06469 ( 1137) link_ALPHA1-3 : bond 0.00812 ( 4) link_ALPHA1-3 : angle 2.05250 ( 12) link_ALPHA1-4 : bond 0.01343 ( 2) link_ALPHA1-4 : angle 2.65302 ( 6) link_ALPHA1-6 : bond 0.00705 ( 4) link_ALPHA1-6 : angle 1.54921 ( 12) link_BETA1-4 : bond 0.00491 ( 9) link_BETA1-4 : angle 1.51141 ( 27) link_NAG-ASN : bond 0.00487 ( 9) link_NAG-ASN : angle 3.62205 ( 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 : 0.498 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: 0.2312 time to fit residues: 7.2319 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 : 0.545 ------------------------------------------------------------------------------- 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: 0.0970 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.056127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.040773 restraints weight = 315569.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.042742 restraints weight = 122457.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.043786 restraints weight = 65705.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.044337 restraints weight = 44845.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.044525 restraints weight = 36213.874| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10266 Z= 0.109 Angle : 0.583 14.158 14058 Z= 0.276 Chirality : 0.042 0.293 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.074 107.586 1891 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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 aren not related in a simple way. whole: 0.28 (0.24), residues: 1227 helix: -1.17 (0.49), residues: 88 sheet: 0.67 (0.21), residues: 583 loop : 0.02 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 331 TYR 0.009 0.001 TYR X 307 PHE 0.011 0.001 PHE X 501 TRP 0.027 0.001 TRP X 513 HIS 0.005 0.001 HIS R 134 Details of bonding type rmsd covalent geometry : bond 0.00241 (10220) covalent geometry : angle 0.53090 (13938) SS BOND : bond 0.00228 ( 18) SS BOND : angle 1.46037 ( 36) hydrogen bonds : bond 0.02670 ( 382) hydrogen bonds : angle 4.90997 ( 1137) link_ALPHA1-3 : bond 0.00783 ( 4) link_ALPHA1-3 : angle 1.96159 ( 12) link_ALPHA1-4 : bond 0.01401 ( 2) link_ALPHA1-4 : angle 2.57171 ( 6) link_ALPHA1-6 : bond 0.00663 ( 4) link_ALPHA1-6 : angle 1.49660 ( 12) link_BETA1-4 : bond 0.00387 ( 9) link_BETA1-4 : angle 1.56333 ( 27) link_NAG-ASN : bond 0.00441 ( 9) link_NAG-ASN : angle 4.67053 ( 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 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.573 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: 22 average time/residue: 0.3004 time to fit residues: 9.3320 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: 20.0000 chunk 16 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.0020 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.055585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.040276 restraints weight = 319284.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.042205 restraints weight = 125548.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.043180 restraints weight = 67980.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.043793 restraints weight = 47241.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.043942 restraints weight = 38364.603| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10266 Z= 0.150 Angle : 0.602 12.178 14058 Z= 0.288 Chirality : 0.042 0.366 1671 Planarity : 0.004 0.044 1746 Dihedral : 7.889 107.601 1891 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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 aren not related in a simple way. whole: 0.24 (0.24), residues: 1227 helix: -1.07 (0.50), residues: 88 sheet: 0.52 (0.21), residues: 576 loop : 0.14 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 106 TYR 0.011 0.001 TYR R 120 PHE 0.010 0.001 PHE X 501 TRP 0.028 0.001 TRP X 513 HIS 0.007 0.001 HIS R 41 Details of bonding type rmsd covalent geometry : bond 0.00319 (10220) covalent geometry : angle 0.55195 (13938) SS BOND : bond 0.00267 ( 18) SS BOND : angle 2.18902 ( 36) hydrogen bonds : bond 0.02760 ( 382) hydrogen bonds : angle 4.88034 ( 1137) link_ALPHA1-3 : bond 0.00796 ( 4) link_ALPHA1-3 : angle 1.87982 ( 12) link_ALPHA1-4 : bond 0.01282 ( 2) link_ALPHA1-4 : angle 2.75483 ( 6) link_ALPHA1-6 : bond 0.00636 ( 4) link_ALPHA1-6 : angle 1.53784 ( 12) link_BETA1-4 : bond 0.00514 ( 9) link_BETA1-4 : angle 1.71780 ( 27) link_NAG-ASN : bond 0.00534 ( 9) link_NAG-ASN : angle 4.18476 ( 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 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.505 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2856 time to fit residues: 8.1660 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 : 0.428 ------------------------------------------------------------------------------- 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: 0.3980 chunk 80 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 40.0000 chunk 21 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4091 r_free = 0.4091 target = 0.055794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.040594 restraints weight = 312380.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.042478 restraints weight = 121977.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.043506 restraints weight = 66209.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.044045 restraints weight = 45226.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.044241 restraints weight = 36517.696| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3368 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= 0.110 Angle : 0.563 9.965 14058 Z= 0.270 Chirality : 0.042 0.284 1671 Planarity : 0.004 0.045 1746 Dihedral : 7.769 106.963 1891 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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 aren not related in a simple way. whole: 0.35 (0.24), residues: 1227 helix: -0.88 (0.51), residues: 88 sheet: 0.59 (0.22), residues: 571 loop : 0.20 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 106 TYR 0.008 0.001 TYR H 150 PHE 0.018 0.001 PHE H 151 TRP 0.024 0.001 TRP X 513 HIS 0.019 0.001 HIS H 181 Details of bonding type rmsd covalent geometry : bond 0.00240 (10220) covalent geometry : angle 0.52234 (13938) SS BOND : bond 0.00235 ( 18) SS BOND : angle 1.83529 ( 36) hydrogen bonds : bond 0.02604 ( 382) hydrogen bonds : angle 4.79154 ( 1137) link_ALPHA1-3 : bond 0.00714 ( 4) link_ALPHA1-3 : angle 1.88388 ( 12) link_ALPHA1-4 : bond 0.01330 ( 2) link_ALPHA1-4 : angle 2.53883 ( 6) link_ALPHA1-6 : bond 0.00651 ( 4) link_ALPHA1-6 : angle 1.45377 ( 12) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.49451 ( 27) link_NAG-ASN : bond 0.00421 ( 9) link_NAG-ASN : angle 3.69981 ( 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 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.564 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: 0.2572 time to fit residues: 7.4348 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 : 0.477 ------------------------------------------------------------------------------- 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: 5.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 52 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4098 r_free = 0.4098 target = 0.055964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.040718 restraints weight = 313643.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.042631 restraints weight = 122150.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.043695 restraints weight = 66065.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.044081 restraints weight = 45037.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.044500 restraints weight = 37603.694| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3436 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 : 0.542 8.999 14058 Z= 0.260 Chirality : 0.042 0.284 1671 Planarity : 0.004 0.045 1746 Dihedral : 7.402 104.931 1891 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 aren not related in a simple way. whole: 0.41 (0.24), residues: 1227 helix: -0.64 (0.53), residues: 88 sheet: 0.67 (0.21), residues: 584 loop : 0.14 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 106 TYR 0.010 0.001 TYR R 120 PHE 0.011 0.001 PHE X 501 TRP 0.024 0.001 TRP X 513 HIS 0.006 0.001 HIS H 181 Details of bonding type rmsd covalent geometry : bond 0.00219 (10220) covalent geometry : angle 0.50839 (13938) SS BOND : bond 0.00205 ( 18) SS BOND : angle 1.53135 ( 36) hydrogen bonds : bond 0.02471 ( 382) hydrogen bonds : angle 4.62323 ( 1137) link_ALPHA1-3 : bond 0.00677 ( 4) link_ALPHA1-3 : angle 1.77999 ( 12) link_ALPHA1-4 : bond 0.01219 ( 2) link_ALPHA1-4 : angle 2.43863 ( 6) link_ALPHA1-6 : bond 0.00673 ( 4) link_ALPHA1-6 : angle 1.37312 ( 12) link_BETA1-4 : bond 0.00445 ( 9) link_BETA1-4 : angle 1.44937 ( 27) link_NAG-ASN : bond 0.00379 ( 9) link_NAG-ASN : angle 3.30668 ( 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 : 0.546 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: 22 average time/residue: 0.3174 time to fit residues: 9.5970 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 : 0.513 ------------------------------------------------------------------------------- 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: 10.0000 chunk 79 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 56 optimal weight: 0.0470 chunk 10 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 overall best weight: 3.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 532 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.054174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.038949 restraints weight = 316505.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.040725 restraints weight = 126429.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.041724 restraints weight = 69287.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.042224 restraints weight = 47491.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.042415 restraints weight = 38837.833| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10266 Z= 0.272 Angle : 0.685 10.440 14058 Z= 0.333 Chirality : 0.042 0.275 1671 Planarity : 0.005 0.047 1746 Dihedral : 7.939 109.499 1891 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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 aren not related in a simple way. whole: -0.07 (0.24), residues: 1227 helix: -0.91 (0.51), residues: 88 sheet: 0.30 (0.21), residues: 565 loop : -0.12 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 106 TYR 0.033 0.002 TYR R 120 PHE 0.011 0.002 PHE H 445 TRP 0.023 0.002 TRP X 513 HIS 0.011 0.002 HIS R 41 Details of bonding type rmsd covalent geometry : bond 0.00553 (10220) covalent geometry : angle 0.64311 (13938) SS BOND : bond 0.00483 ( 18) SS BOND : angle 1.73299 ( 36) hydrogen bonds : bond 0.03445 ( 382) hydrogen bonds : angle 5.09166 ( 1137) link_ALPHA1-3 : bond 0.00934 ( 4) link_ALPHA1-3 : angle 1.91852 ( 12) link_ALPHA1-4 : bond 0.01251 ( 2) link_ALPHA1-4 : angle 3.49588 ( 6) link_ALPHA1-6 : bond 0.00666 ( 4) link_ALPHA1-6 : angle 1.69477 ( 12) link_BETA1-4 : bond 0.00661 ( 9) link_BETA1-4 : angle 2.13611 ( 27) link_NAG-ASN : bond 0.00794 ( 9) link_NAG-ASN : angle 4.10124 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4681.88 seconds wall clock time: 80 minutes 23.92 seconds (4823.92 seconds total)