Starting phenix.real_space_refine on Tue Jun 17 07:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1c_16378/06_2025/8c1c_16378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1c_16378/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1c_16378/06_2025/8c1c_16378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1c_16378/06_2025/8c1c_16378.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1c_16378/06_2025/8c1c_16378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1c_16378/06_2025/8c1c_16378.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.68, per 1000 atoms: 0.61 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: 5.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.94 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: 7.55 Time building geometry restraints manager: 6.44 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: 0.010 Normalize map: mean=0, sd=1: 4.030 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: 0.350 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.820 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.054 0.004 TRP R 13 HIS 0.023 0.003 HIS R 108 PHE 0.050 0.004 PHE R 17 TYR 0.047 0.003 TYR R 149 ARG 0.011 0.001 ARG R 15 Details of bonding type rmsd link_NAG-ASN : bond 0.01433 ( 9) link_NAG-ASN : angle 9.19204 ( 27) 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_ALPHA1-3 : bond 0.00586 ( 4) link_ALPHA1-3 : angle 1.79926 ( 12) hydrogen bonds : bond 0.09507 ( 382) hydrogen bonds : angle 6.50635 ( 1137) SS BOND : bond 0.01041 ( 18) SS BOND : angle 4.28482 ( 36) covalent geometry : bond 0.00761 (10220) covalent geometry : angle 1.21214 (13938) *********************** 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 : 1.507 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: 0.6426 time to fit residues: 26.0136 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 : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.058211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.042967 restraints weight = 296437.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.044984 restraints weight = 117862.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.046050 restraints weight = 62768.724| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1062 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= 0.157 Angle : 0.665 17.058 14058 Z= 0.320 Chirality : 0.044 0.314 1671 Planarity : 0.005 0.049 1746 Dihedral : 10.698 110.282 1891 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1227 helix: -1.77 (0.46), residues: 88 sheet: 0.95 (0.21), residues: 587 loop : -0.15 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 513 HIS 0.009 0.001 HIS R 134 PHE 0.012 0.001 PHE R 17 TYR 0.014 0.001 TYR R 120 ARG 0.003 0.000 ARG H 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 9) link_NAG-ASN : angle 5.40935 ( 27) link_ALPHA1-4 : bond 0.01503 ( 2) link_ALPHA1-4 : angle 2.86897 ( 6) link_ALPHA1-6 : bond 0.00869 ( 4) link_ALPHA1-6 : angle 1.81058 ( 12) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.99218 ( 27) link_ALPHA1-3 : bond 0.00777 ( 4) link_ALPHA1-3 : angle 2.40381 ( 12) hydrogen bonds : bond 0.03500 ( 382) hydrogen bonds : angle 5.42876 ( 1137) SS BOND : bond 0.00357 ( 18) SS BOND : angle 1.21725 ( 36) covalent geometry : bond 0.00321 (10220) covalent geometry : angle 0.60493 (13938) *********************** 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 : 1.572 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: 0.5472 time to fit residues: 20.5526 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 : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.3980 chunk 71 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.057381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.042186 restraints weight = 305965.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.044188 restraints weight = 119700.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.045237 restraints weight = 63488.758| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10266 Z= 0.142 Angle : 0.626 11.405 14058 Z= 0.297 Chirality : 0.043 0.278 1671 Planarity : 0.005 0.070 1746 Dihedral : 9.466 110.441 1891 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1227 helix: -1.64 (0.44), residues: 89 sheet: 1.03 (0.21), residues: 582 loop : -0.04 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 513 HIS 0.010 0.001 HIS R 41 PHE 0.010 0.001 PHE H 151 TYR 0.013 0.001 TYR H 182 ARG 0.006 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 9) link_NAG-ASN : angle 4.12300 ( 27) link_ALPHA1-4 : bond 0.01328 ( 2) link_ALPHA1-4 : angle 2.75767 ( 6) link_ALPHA1-6 : bond 0.00868 ( 4) link_ALPHA1-6 : angle 1.88864 ( 12) link_BETA1-4 : bond 0.00433 ( 9) link_BETA1-4 : angle 1.73084 ( 27) link_ALPHA1-3 : bond 0.01044 ( 4) link_ALPHA1-3 : angle 1.98716 ( 12) hydrogen bonds : bond 0.03049 ( 382) hydrogen bonds : angle 5.08131 ( 1137) SS BOND : bond 0.00554 ( 18) SS BOND : angle 1.54653 ( 36) covalent geometry : bond 0.00297 (10220) covalent geometry : angle 0.58377 (13938) *********************** 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 : 1.820 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: 0.5768 time to fit residues: 19.1418 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 : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 298 GLN ** H 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN ** X 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.055132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.039702 restraints weight = 308160.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.041511 restraints weight = 124744.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.042539 restraints weight = 68345.700| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10266 Z= 0.296 Angle : 0.780 15.565 14058 Z= 0.374 Chirality : 0.047 0.757 1671 Planarity : 0.005 0.047 1746 Dihedral : 9.133 110.992 1891 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1227 helix: -1.67 (0.44), residues: 89 sheet: 0.56 (0.21), residues: 577 loop : -0.49 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 513 HIS 0.018 0.002 HIS R 41 PHE 0.025 0.002 PHE H 151 TYR 0.018 0.002 TYR R 120 ARG 0.011 0.001 ARG H 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00955 ( 9) link_NAG-ASN : angle 5.09954 ( 27) link_ALPHA1-4 : bond 0.01393 ( 2) link_ALPHA1-4 : angle 3.85114 ( 6) link_ALPHA1-6 : bond 0.00909 ( 4) link_ALPHA1-6 : angle 1.63076 ( 12) link_BETA1-4 : bond 0.00740 ( 9) link_BETA1-4 : angle 2.68120 ( 27) link_ALPHA1-3 : bond 0.00853 ( 4) link_ALPHA1-3 : angle 2.27659 ( 12) hydrogen bonds : bond 0.03651 ( 382) hydrogen bonds : angle 5.38184 ( 1137) SS BOND : bond 0.00762 ( 18) SS BOND : angle 2.56296 ( 36) covalent geometry : bond 0.00597 (10220) covalent geometry : angle 0.72079 (13938) *********************** 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: 1 poor density : 20 time to evaluate : 1.575 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: 1 outliers final: 0 residues processed: 21 average time/residue: 0.5249 time to fit residues: 17.0744 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 : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.055790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.040386 restraints weight = 308916.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.042227 restraints weight = 123339.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.043272 restraints weight = 66971.910| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10266 Z= 0.156 Angle : 0.645 17.246 14058 Z= 0.306 Chirality : 0.043 0.325 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.695 110.414 1891 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1227 helix: -1.56 (0.46), residues: 89 sheet: 0.56 (0.21), residues: 582 loop : -0.27 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 513 HIS 0.015 0.001 HIS H 181 PHE 0.017 0.001 PHE H 151 TYR 0.013 0.001 TYR X 307 ARG 0.005 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 9) link_NAG-ASN : angle 5.49134 ( 27) link_ALPHA1-4 : bond 0.01386 ( 2) link_ALPHA1-4 : angle 2.77712 ( 6) link_ALPHA1-6 : bond 0.00753 ( 4) link_ALPHA1-6 : angle 1.58507 ( 12) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 1.63789 ( 27) link_ALPHA1-3 : bond 0.00917 ( 4) link_ALPHA1-3 : angle 2.11966 ( 12) hydrogen bonds : bond 0.03011 ( 382) hydrogen bonds : angle 5.16302 ( 1137) SS BOND : bond 0.00381 ( 18) SS BOND : angle 1.99240 ( 36) covalent geometry : bond 0.00320 (10220) covalent geometry : angle 0.57996 (13938) *********************** 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 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 1.608 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: 22 average time/residue: 0.6338 time to fit residues: 20.4037 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 : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.055637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.040270 restraints weight = 308549.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.042107 restraints weight = 123139.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.043138 restraints weight = 66679.409| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10266 Z= 0.155 Angle : 0.599 10.150 14058 Z= 0.288 Chirality : 0.042 0.342 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.298 108.886 1891 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1227 helix: -1.32 (0.47), residues: 89 sheet: 0.52 (0.21), residues: 591 loop : -0.10 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 513 HIS 0.010 0.001 HIS H 181 PHE 0.010 0.001 PHE X 501 TYR 0.012 0.001 TYR R 120 ARG 0.004 0.000 ARG H 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 9) link_NAG-ASN : angle 3.94838 ( 27) link_ALPHA1-4 : bond 0.01384 ( 2) link_ALPHA1-4 : angle 2.90940 ( 6) link_ALPHA1-6 : bond 0.00693 ( 4) link_ALPHA1-6 : angle 1.58606 ( 12) link_BETA1-4 : bond 0.00473 ( 9) link_BETA1-4 : angle 1.68311 ( 27) link_ALPHA1-3 : bond 0.00851 ( 4) link_ALPHA1-3 : angle 2.01917 ( 12) hydrogen bonds : bond 0.02918 ( 382) hydrogen bonds : angle 5.06449 ( 1137) SS BOND : bond 0.00349 ( 18) SS BOND : angle 1.25975 ( 36) covalent geometry : bond 0.00320 (10220) covalent geometry : angle 0.55922 (13938) *********************** 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 : 1.565 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: 21 average time/residue: 0.6285 time to fit residues: 19.2134 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 : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 30.0000 chunk 100 optimal weight: 0.0570 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 40.0000 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 overall best weight: 2.2104 ------------------------------------------------------------------------------- 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 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 389 GLN ** X 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 532 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.055111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.039304 restraints weight = 316057.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.041153 restraints weight = 125652.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.042156 restraints weight = 69087.382| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10266 Z= 0.206 Angle : 0.671 16.843 14058 Z= 0.322 Chirality : 0.042 0.408 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.352 109.859 1891 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1227 helix: -1.37 (0.48), residues: 89 sheet: 0.36 (0.21), residues: 567 loop : -0.19 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP X 513 HIS 0.010 0.002 HIS R 41 PHE 0.010 0.001 PHE X 501 TYR 0.015 0.002 TYR R 120 ARG 0.005 0.001 ARG H 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00859 ( 9) link_NAG-ASN : angle 5.60479 ( 27) link_ALPHA1-4 : bond 0.01361 ( 2) link_ALPHA1-4 : angle 3.07213 ( 6) link_ALPHA1-6 : bond 0.00655 ( 4) link_ALPHA1-6 : angle 1.59963 ( 12) link_BETA1-4 : bond 0.00558 ( 9) link_BETA1-4 : angle 1.84545 ( 27) link_ALPHA1-3 : bond 0.00871 ( 4) link_ALPHA1-3 : angle 1.95249 ( 12) hydrogen bonds : bond 0.03123 ( 382) hydrogen bonds : angle 5.18700 ( 1137) SS BOND : bond 0.00311 ( 18) SS BOND : angle 2.28934 ( 36) covalent geometry : bond 0.00427 (10220) covalent geometry : angle 0.60341 (13938) *********************** 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 23 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 1.676 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: 23 average time/residue: 0.6879 time to fit residues: 22.7246 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 : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 532 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 = 0.4077 r_free = 0.4077 target = 0.055485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.040222 restraints weight = 320979.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.042066 restraints weight = 125658.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.043111 restraints weight = 68357.367| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10266 Z= 0.137 Angle : 0.605 13.708 14058 Z= 0.289 Chirality : 0.042 0.365 1671 Planarity : 0.004 0.045 1746 Dihedral : 8.071 108.577 1891 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1227 helix: -1.15 (0.49), residues: 88 sheet: 0.34 (0.21), residues: 571 loop : 0.01 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP X 513 HIS 0.007 0.001 HIS H 181 PHE 0.011 0.001 PHE X 501 TYR 0.010 0.001 TYR X 307 ARG 0.003 0.000 ARG X 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 9) link_NAG-ASN : angle 4.70914 ( 27) link_ALPHA1-4 : bond 0.01362 ( 2) link_ALPHA1-4 : angle 2.66804 ( 6) link_ALPHA1-6 : bond 0.00664 ( 4) link_ALPHA1-6 : angle 1.50039 ( 12) link_BETA1-4 : bond 0.00456 ( 9) link_BETA1-4 : angle 1.52868 ( 27) link_ALPHA1-3 : bond 0.00769 ( 4) link_ALPHA1-3 : angle 1.91047 ( 12) hydrogen bonds : bond 0.02830 ( 382) hydrogen bonds : angle 5.02730 ( 1137) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.79516 ( 36) covalent geometry : bond 0.00286 (10220) covalent geometry : angle 0.55207 (13938) *********************** 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 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 1.550 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: 22 average time/residue: 0.6664 time to fit residues: 20.6958 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 : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 90 optimal weight: 0.0470 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.055808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.040522 restraints weight = 316352.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.042407 restraints weight = 124205.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.043432 restraints weight = 67394.757| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10266 Z= 0.106 Angle : 0.571 11.172 14058 Z= 0.274 Chirality : 0.042 0.288 1671 Planarity : 0.004 0.046 1746 Dihedral : 7.813 107.072 1891 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1227 helix: -1.05 (0.50), residues: 88 sheet: 0.41 (0.21), residues: 576 loop : 0.19 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP X 513 HIS 0.005 0.001 HIS H 181 PHE 0.011 0.001 PHE X 501 TYR 0.008 0.001 TYR X 307 ARG 0.002 0.000 ARG X 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 9) link_NAG-ASN : angle 4.17755 ( 27) link_ALPHA1-4 : bond 0.01306 ( 2) link_ALPHA1-4 : angle 2.47327 ( 6) link_ALPHA1-6 : bond 0.00604 ( 4) link_ALPHA1-6 : angle 1.39922 ( 12) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.49039 ( 27) link_ALPHA1-3 : bond 0.00702 ( 4) link_ALPHA1-3 : angle 1.86381 ( 12) hydrogen bonds : bond 0.02717 ( 382) hydrogen bonds : angle 4.89066 ( 1137) SS BOND : bond 0.00188 ( 18) SS BOND : angle 1.34737 ( 36) covalent geometry : bond 0.00233 (10220) covalent geometry : angle 0.52834 (13938) *********************** 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 23 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 1.515 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: 23 average time/residue: 0.6546 time to fit residues: 21.3649 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 : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 79 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.055717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.040493 restraints weight = 315962.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.042362 restraints weight = 124173.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.043391 restraints weight = 66997.615| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3574 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= 0.110 Angle : 0.561 10.508 14058 Z= 0.268 Chirality : 0.042 0.293 1671 Planarity : 0.004 0.048 1746 Dihedral : 7.585 106.384 1891 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1227 helix: -1.03 (0.49), residues: 94 sheet: 0.41 (0.21), residues: 578 loop : 0.19 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP X 513 HIS 0.005 0.001 HIS X 205 PHE 0.011 0.001 PHE X 501 TYR 0.008 0.001 TYR X 307 ARG 0.003 0.000 ARG H 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 9) link_NAG-ASN : angle 3.95988 ( 27) link_ALPHA1-4 : bond 0.01252 ( 2) link_ALPHA1-4 : angle 2.50556 ( 6) link_ALPHA1-6 : bond 0.00658 ( 4) link_ALPHA1-6 : angle 1.43414 ( 12) link_BETA1-4 : bond 0.00406 ( 9) link_BETA1-4 : angle 1.52173 ( 27) link_ALPHA1-3 : bond 0.00714 ( 4) link_ALPHA1-3 : angle 1.81298 ( 12) hydrogen bonds : bond 0.02623 ( 382) hydrogen bonds : angle 4.80358 ( 1137) SS BOND : bond 0.00234 ( 18) SS BOND : angle 1.27793 ( 36) covalent geometry : bond 0.00239 (10220) covalent geometry : angle 0.52025 (13938) ********************** 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 : 1.688 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: 22 average time/residue: 0.7312 time to fit residues: 23.0896 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 : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.055476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.039758 restraints weight = 313971.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.041650 restraints weight = 123560.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.042678 restraints weight = 67306.998| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10266 Z= 0.120 Angle : 0.561 9.742 14058 Z= 0.268 Chirality : 0.041 0.278 1671 Planarity : 0.004 0.046 1746 Dihedral : 7.435 106.273 1891 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1227 helix: -0.93 (0.51), residues: 94 sheet: 0.37 (0.21), residues: 582 loop : 0.19 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP X 513 HIS 0.004 0.001 HIS R 41 PHE 0.011 0.001 PHE X 501 TYR 0.009 0.001 TYR X 307 ARG 0.003 0.000 ARG H 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 9) link_NAG-ASN : angle 3.74811 ( 27) link_ALPHA1-4 : bond 0.01231 ( 2) link_ALPHA1-4 : angle 2.54139 ( 6) link_ALPHA1-6 : bond 0.00659 ( 4) link_ALPHA1-6 : angle 1.41568 ( 12) link_BETA1-4 : bond 0.00386 ( 9) link_BETA1-4 : angle 1.52547 ( 27) link_ALPHA1-3 : bond 0.00693 ( 4) link_ALPHA1-3 : angle 1.79313 ( 12) hydrogen bonds : bond 0.02615 ( 382) hydrogen bonds : angle 4.70716 ( 1137) SS BOND : bond 0.00203 ( 18) SS BOND : angle 1.20536 ( 36) covalent geometry : bond 0.00258 (10220) covalent geometry : angle 0.52378 (13938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8543.70 seconds wall clock time: 145 minutes 52.98 seconds (8752.98 seconds total)