Starting phenix.real_space_refine on Tue May 20 07:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1c_16378/05_2025/8c1c_16378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1c_16378/05_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_16378/05_2025/8c1c_16378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1c_16378/05_2025/8c1c_16378.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1c_16378/05_2025/8c1c_16378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1c_16378/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.61, per 1000 atoms: 0.50 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: 5.01 Conformation dependent library (CDL) restraints added in 1.4 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: 2.12 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: 7.63 Time building geometry restraints manager: 5.97 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.340 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.520 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.620 ------------------------------------------------------------------------------- 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 : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.6543 time to fit residues: 26.3276 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 : 1.450 ------------------------------------------------------------------------------- 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 = 68)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.042966 restraints weight = 296439.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.045011 restraints weight = 117537.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.046108 restraints weight = 62432.569| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 17.056 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 0.00664 ( 9) link_NAG-ASN : angle 5.40927 ( 27) link_ALPHA1-4 : bond 0.01503 ( 2) link_ALPHA1-4 : angle 2.86891 ( 6) link_ALPHA1-6 : bond 0.00869 ( 4) link_ALPHA1-6 : angle 1.81060 ( 12) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.99206 ( 27) link_ALPHA1-3 : bond 0.00777 ( 4) link_ALPHA1-3 : angle 2.40393 ( 12) hydrogen bonds : bond 0.03500 ( 382) hydrogen bonds : angle 5.42876 ( 1137) SS BOND : bond 0.00357 ( 18) SS BOND : angle 1.21713 ( 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 : 1.582 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: 0.5532 time to fit residues: 20.8130 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 : 1.611 ------------------------------------------------------------------------------- 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: 0.7980 chunk 71 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.057119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.041946 restraints weight = 306951.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.043881 restraints weight = 121576.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.044909 restraints weight = 65266.378| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1674 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= 0.164 Angle : 0.641 11.086 14058 Z= 0.306 Chirality : 0.043 0.318 1671 Planarity : 0.005 0.081 1746 Dihedral : 9.619 111.399 1891 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.24), residues: 1227 helix: -1.69 (0.44), residues: 89 sheet: 0.98 (0.21), residues: 582 loop : -0.09 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 513 HIS 0.012 0.001 HIS R 41 PHE 0.010 0.001 PHE H 151 TYR 0.015 0.001 TYR R 120 ARG 0.005 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 9) link_NAG-ASN : angle 4.16699 ( 27) link_ALPHA1-4 : bond 0.01562 ( 2) link_ALPHA1-4 : angle 3.00953 ( 6) link_ALPHA1-6 : bond 0.00829 ( 4) link_ALPHA1-6 : angle 1.87029 ( 12) link_BETA1-4 : bond 0.00487 ( 9) link_BETA1-4 : angle 1.81580 ( 27) link_ALPHA1-3 : bond 0.01106 ( 4) link_ALPHA1-3 : angle 2.01367 ( 12) hydrogen bonds : bond 0.03151 ( 382) hydrogen bonds : angle 5.15157 ( 1137) SS BOND : bond 0.00395 ( 18) SS BOND : angle 1.79515 ( 36) covalent geometry : bond 0.00339 (10220) covalent geometry : angle 0.59687 (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 : 1.563 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: 0.5866 time to fit residues: 19.0792 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 : 2.008 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.055332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.039880 restraints weight = 308008.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.041697 restraints weight = 122899.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.042718 restraints weight = 66766.217| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10266 Z= 0.264 Angle : 0.726 13.458 14058 Z= 0.348 Chirality : 0.045 0.601 1671 Planarity : 0.005 0.047 1746 Dihedral : 8.949 109.151 1891 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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 (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: -0.09 (0.24), residues: 1227 helix: -1.60 (0.45), residues: 89 sheet: 0.56 (0.21), residues: 586 loop : -0.38 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 513 HIS 0.018 0.002 HIS R 41 PHE 0.023 0.002 PHE H 151 TYR 0.017 0.002 TYR R 120 ARG 0.009 0.001 ARG H 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 9) link_NAG-ASN : angle 4.97984 ( 27) link_ALPHA1-4 : bond 0.01196 ( 2) link_ALPHA1-4 : angle 3.55994 ( 6) link_ALPHA1-6 : bond 0.00868 ( 4) link_ALPHA1-6 : angle 1.62704 ( 12) link_BETA1-4 : bond 0.00652 ( 9) link_BETA1-4 : angle 2.38459 ( 27) link_ALPHA1-3 : bond 0.01091 ( 4) link_ALPHA1-3 : angle 2.29745 ( 12) hydrogen bonds : bond 0.03455 ( 382) hydrogen bonds : angle 5.30447 ( 1137) SS BOND : bond 0.00514 ( 18) SS BOND : angle 2.06938 ( 36) covalent geometry : bond 0.00531 (10220) covalent geometry : angle 0.67050 (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 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 1.528 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: 20 average time/residue: 0.5550 time to fit residues: 16.9358 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 : 1.446 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 0.0050 chunk 56 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.056297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.040996 restraints weight = 318011.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.042944 restraints weight = 125778.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.043954 restraints weight = 68026.573| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2591 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= 0.124 Angle : 0.610 14.250 14058 Z= 0.288 Chirality : 0.043 0.311 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.555 109.762 1891 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: 0.17 (0.24), residues: 1227 helix: -1.46 (0.47), residues: 89 sheet: 0.64 (0.21), residues: 592 loop : -0.08 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 513 HIS 0.006 0.001 HIS R 41 PHE 0.012 0.001 PHE H 151 TYR 0.011 0.001 TYR X 307 ARG 0.004 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 9) link_NAG-ASN : angle 4.97242 ( 27) link_ALPHA1-4 : bond 0.01486 ( 2) link_ALPHA1-4 : angle 2.67726 ( 6) link_ALPHA1-6 : bond 0.00735 ( 4) link_ALPHA1-6 : angle 1.55472 ( 12) link_BETA1-4 : bond 0.00434 ( 9) link_BETA1-4 : angle 1.56585 ( 27) link_ALPHA1-3 : bond 0.00897 ( 4) link_ALPHA1-3 : angle 2.15061 ( 12) hydrogen bonds : bond 0.02837 ( 382) hydrogen bonds : angle 5.04089 ( 1137) SS BOND : bond 0.00360 ( 18) SS BOND : angle 1.48640 ( 36) covalent geometry : bond 0.00262 (10220) covalent geometry : angle 0.55463 (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 : 1.542 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: 0.6515 time to fit residues: 20.8181 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 : 1.687 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 389 GLN X 465 ASN ** 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 = 0.4078 r_free = 0.4078 target = 0.055355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.040029 restraints weight = 317994.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.041866 restraints weight = 126485.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.042868 restraints weight = 68721.733| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10266 Z= 0.206 Angle : 0.645 10.065 14058 Z= 0.312 Chirality : 0.042 0.393 1671 Planarity : 0.004 0.045 1746 Dihedral : 8.386 109.645 1891 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.47), residues: 89 sheet: 0.47 (0.21), residues: 582 loop : -0.24 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP X 513 HIS 0.012 0.002 HIS R 41 PHE 0.010 0.001 PHE R 40 TYR 0.014 0.002 TYR X 307 ARG 0.007 0.000 ARG H 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 9) link_NAG-ASN : angle 4.19074 ( 27) link_ALPHA1-4 : bond 0.01320 ( 2) link_ALPHA1-4 : angle 3.17082 ( 6) link_ALPHA1-6 : bond 0.00697 ( 4) link_ALPHA1-6 : angle 1.64387 ( 12) link_BETA1-4 : bond 0.00546 ( 9) link_BETA1-4 : angle 1.94486 ( 27) link_ALPHA1-3 : bond 0.00892 ( 4) link_ALPHA1-3 : angle 2.06332 ( 12) hydrogen bonds : bond 0.03111 ( 382) hydrogen bonds : angle 5.13911 ( 1137) SS BOND : bond 0.00391 ( 18) SS BOND : angle 1.73688 ( 36) covalent geometry : bond 0.00422 (10220) covalent geometry : angle 0.60026 (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 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 1.473 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: 0.5550 time to fit residues: 16.7391 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 : 1.468 ------------------------------------------------------------------------------- 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: 2.9990 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 40.0000 chunk 47 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 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 = 0.4056 r_free = 0.4056 target = 0.054899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.039526 restraints weight = 317770.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.041329 restraints weight = 125946.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.042299 restraints weight = 68734.729| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10266 Z= 0.219 Angle : 0.691 18.633 14058 Z= 0.331 Chirality : 0.042 0.279 1671 Planarity : 0.005 0.046 1746 Dihedral : 8.506 110.425 1891 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.47), residues: 88 sheet: 0.32 (0.21), residues: 566 loop : -0.27 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 513 HIS 0.010 0.002 HIS R 41 PHE 0.011 0.001 PHE X 501 TYR 0.023 0.002 TYR R 120 ARG 0.008 0.001 ARG X 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00769 ( 9) link_NAG-ASN : angle 5.72184 ( 27) link_ALPHA1-4 : bond 0.01353 ( 2) link_ALPHA1-4 : angle 3.03458 ( 6) link_ALPHA1-6 : bond 0.00666 ( 4) link_ALPHA1-6 : angle 1.59409 ( 12) link_BETA1-4 : bond 0.00475 ( 9) link_BETA1-4 : angle 1.81632 ( 27) link_ALPHA1-3 : bond 0.00842 ( 4) link_ALPHA1-3 : angle 1.92493 ( 12) hydrogen bonds : bond 0.03252 ( 382) hydrogen bonds : angle 5.27925 ( 1137) SS BOND : bond 0.00467 ( 18) SS BOND : angle 2.13296 ( 36) covalent geometry : bond 0.00452 (10220) covalent geometry : angle 0.62488 (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 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 1.503 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: 0.5970 time to fit residues: 19.1501 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 : 1.576 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4072 r_free = 0.4072 target = 0.055305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.040048 restraints weight = 320372.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.041904 restraints weight = 125527.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.042941 restraints weight = 68086.362| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10266 Z= 0.140 Angle : 0.617 14.336 14058 Z= 0.296 Chirality : 0.042 0.358 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.165 108.965 1891 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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: -0.01 (0.24), residues: 1227 helix: -1.16 (0.49), residues: 88 sheet: 0.31 (0.21), residues: 572 loop : 0.01 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 513 HIS 0.016 0.001 HIS H 181 PHE 0.012 0.001 PHE H 151 TYR 0.026 0.001 TYR R 120 ARG 0.007 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 9) link_NAG-ASN : angle 4.67240 ( 27) link_ALPHA1-4 : bond 0.01392 ( 2) link_ALPHA1-4 : angle 2.71497 ( 6) link_ALPHA1-6 : bond 0.00657 ( 4) link_ALPHA1-6 : angle 1.48155 ( 12) link_BETA1-4 : bond 0.00461 ( 9) link_BETA1-4 : angle 1.58746 ( 27) link_ALPHA1-3 : bond 0.00869 ( 4) link_ALPHA1-3 : angle 1.95500 ( 12) hydrogen bonds : bond 0.02881 ( 382) hydrogen bonds : angle 5.07776 ( 1137) SS BOND : bond 0.00282 ( 18) SS BOND : angle 2.31351 ( 36) covalent geometry : bond 0.00297 (10220) covalent geometry : angle 0.56085 (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 : 1.517 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: 0.6021 time to fit residues: 19.3701 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 : 1.430 ------------------------------------------------------------------------------- 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: 2.9990 chunk 99 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.055370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.040123 restraints weight = 316866.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.041997 restraints weight = 123984.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.043015 restraints weight = 66989.273| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10266 Z= 0.126 Angle : 0.589 12.079 14058 Z= 0.283 Chirality : 0.042 0.299 1671 Planarity : 0.004 0.046 1746 Dihedral : 7.956 108.033 1891 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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 (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: -1.04 (0.50), residues: 88 sheet: 0.34 (0.21), residues: 569 loop : 0.08 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 513 HIS 0.011 0.001 HIS H 181 PHE 0.011 0.001 PHE X 501 TYR 0.021 0.001 TYR R 120 ARG 0.005 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 9) link_NAG-ASN : angle 4.21768 ( 27) link_ALPHA1-4 : bond 0.01362 ( 2) link_ALPHA1-4 : angle 2.63880 ( 6) link_ALPHA1-6 : bond 0.00651 ( 4) link_ALPHA1-6 : angle 1.45492 ( 12) link_BETA1-4 : bond 0.00453 ( 9) link_BETA1-4 : angle 1.53794 ( 27) link_ALPHA1-3 : bond 0.00708 ( 4) link_ALPHA1-3 : angle 1.83844 ( 12) hydrogen bonds : bond 0.02810 ( 382) hydrogen bonds : angle 4.97549 ( 1137) SS BOND : bond 0.00303 ( 18) SS BOND : angle 1.70586 ( 36) covalent geometry : bond 0.00270 (10220) covalent geometry : angle 0.54405 (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 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 1.467 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: 0.6246 time to fit residues: 18.3509 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 : 1.457 ------------------------------------------------------------------------------- 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: 7.9990 chunk 36 optimal weight: 0.0670 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.055454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.040179 restraints weight = 318238.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.042044 restraints weight = 124029.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.043087 restraints weight = 67267.139| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10266 Z= 0.114 Angle : 0.565 10.107 14058 Z= 0.271 Chirality : 0.042 0.293 1671 Planarity : 0.004 0.046 1746 Dihedral : 7.639 106.677 1891 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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: 0.10 (0.24), residues: 1227 helix: -0.94 (0.50), residues: 94 sheet: 0.36 (0.21), residues: 573 loop : 0.11 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 513 HIS 0.008 0.001 HIS H 181 PHE 0.011 0.001 PHE X 501 TYR 0.021 0.001 TYR R 120 ARG 0.004 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 9) link_NAG-ASN : angle 3.76420 ( 27) link_ALPHA1-4 : bond 0.01301 ( 2) link_ALPHA1-4 : angle 2.53951 ( 6) link_ALPHA1-6 : bond 0.00664 ( 4) link_ALPHA1-6 : angle 1.38593 ( 12) link_BETA1-4 : bond 0.00451 ( 9) link_BETA1-4 : angle 1.48260 ( 27) link_ALPHA1-3 : bond 0.00712 ( 4) link_ALPHA1-3 : angle 1.80371 ( 12) hydrogen bonds : bond 0.02643 ( 382) hydrogen bonds : angle 4.81058 ( 1137) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.43371 ( 36) covalent geometry : bond 0.00248 (10220) covalent geometry : angle 0.52728 (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 20 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 1.533 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: 0.6704 time to fit residues: 19.5535 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 : 1.472 ------------------------------------------------------------------------------- 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: 0.9990 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 0.1980 chunk 88 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.055585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.040395 restraints weight = 314533.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.042261 restraints weight = 122510.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.043310 restraints weight = 65977.834| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10266 Z= 0.100 Angle : 0.551 9.374 14058 Z= 0.265 Chirality : 0.041 0.280 1671 Planarity : 0.004 0.045 1746 Dihedral : 7.421 105.469 1891 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: 0.19 (0.24), residues: 1227 helix: -0.83 (0.51), residues: 94 sheet: 0.41 (0.21), residues: 571 loop : 0.17 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 513 HIS 0.007 0.001 HIS H 181 PHE 0.011 0.001 PHE X 501 TYR 0.018 0.001 TYR R 120 ARG 0.003 0.000 ARG R 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 9) link_NAG-ASN : angle 3.43908 ( 27) link_ALPHA1-4 : bond 0.01201 ( 2) link_ALPHA1-4 : angle 2.39014 ( 6) link_ALPHA1-6 : bond 0.00702 ( 4) link_ALPHA1-6 : angle 1.37960 ( 12) link_BETA1-4 : bond 0.00444 ( 9) link_BETA1-4 : angle 1.44856 ( 27) link_ALPHA1-3 : bond 0.00683 ( 4) link_ALPHA1-3 : angle 1.77930 ( 12) hydrogen bonds : bond 0.02575 ( 382) hydrogen bonds : angle 4.67180 ( 1137) SS BOND : bond 0.00209 ( 18) SS BOND : angle 1.35732 ( 36) covalent geometry : bond 0.00224 (10220) covalent geometry : angle 0.51713 (13938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8220.45 seconds wall clock time: 142 minutes 8.93 seconds (8528.93 seconds total)