Starting phenix.real_space_refine on Tue Nov 19 16:25:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1c_16378/11_2024/8c1c_16378.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1c_16378/11_2024/8c1c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1c_16378/11_2024/8c1c_16378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1c_16378/11_2024/8c1c_16378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1c_16378/11_2024/8c1c_16378.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1c_16378/11_2024/8c1c_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-5513/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: 10.45, per 1000 atoms: 0.54 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: 5.64 Conformation dependent library (CDL) restraints added in 1.6 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: 2.11 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: 8.08 Time building geometry restraints manager: 6.51 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: 4.160 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: 0.400 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 44.880 Find NCS groups from input model: 0.400 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.900 ------------------------------------------------------------------------------- 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 10220 Z= 0.503 Angle : 1.212 11.420 13938 Z= 0.637 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 *********************** 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 : 1.691 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: 0.6502 time to fit residues: 26.7973 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 : 1.579 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10220 Z= 0.205 Angle : 0.607 8.841 13938 Z= 0.307 Chirality : 0.043 0.256 1671 Planarity : 0.005 0.049 1746 Dihedral : 10.809 110.886 1891 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.33 (0.24), residues: 1227 helix: -1.78 (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 0.010 0.001 PHE H 151 TYR 0.012 0.001 TYR R 120 ARG 0.003 0.000 ARG H 348 *********************** 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 : 1.543 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: 0.5801 time to fit residues: 21.7672 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 : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10220 Z= 0.193 Angle : 0.570 9.462 13938 Z= 0.281 Chirality : 0.043 0.296 1671 Planarity : 0.005 0.050 1746 Dihedral : 9.656 110.152 1891 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.24), residues: 1227 helix: -1.67 (0.45), residues: 89 sheet: 1.04 (0.21), residues: 581 loop : -0.04 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 513 HIS 0.008 0.001 HIS R 41 PHE 0.010 0.001 PHE H 151 TYR 0.011 0.001 TYR H 182 ARG 0.005 0.000 ARG R 106 *********************** 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 23 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 1.767 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: 23 average time/residue: 0.5920 time to fit residues: 20.4042 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 : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10220 Z= 0.322 Angle : 0.661 11.765 13938 Z= 0.328 Chirality : 0.045 0.525 1671 Planarity : 0.005 0.047 1746 Dihedral : 8.877 110.046 1891 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 0.07 (0.24), residues: 1227 helix: -1.54 (0.46), residues: 89 sheet: 0.67 (0.21), residues: 585 loop : -0.27 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 513 HIS 0.017 0.002 HIS R 41 PHE 0.013 0.002 PHE R 17 TYR 0.028 0.002 TYR R 80 ARG 0.012 0.001 ARG H 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 1.583 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: 0.6318 time to fit residues: 19.8128 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 : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10220 Z= 0.229 Angle : 0.580 10.940 13938 Z= 0.289 Chirality : 0.043 0.343 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.543 109.959 1891 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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: 0.07 (0.24), residues: 1227 helix: -1.49 (0.46), residues: 89 sheet: 0.57 (0.21), residues: 591 loop : -0.16 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 513 HIS 0.009 0.001 HIS R 41 PHE 0.017 0.001 PHE H 151 TYR 0.014 0.001 TYR X 307 ARG 0.005 0.000 ARG R 106 *********************** 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 21 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 GLU cc_start: 0.5946 (tp30) cc_final: 0.5741 (tp30) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.6539 time to fit residues: 20.0005 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 : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10220 Z= 0.196 Angle : 0.548 9.668 13938 Z= 0.275 Chirality : 0.042 0.324 1671 Planarity : 0.004 0.046 1746 Dihedral : 8.184 108.377 1891 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.24), residues: 1227 helix: -1.41 (0.47), residues: 89 sheet: 0.58 (0.21), residues: 591 loop : -0.05 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP X 513 HIS 0.007 0.001 HIS R 41 PHE 0.010 0.001 PHE X 501 TYR 0.011 0.001 TYR X 307 ARG 0.004 0.000 ARG H 331 *********************** 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 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 1.549 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: 0.6418 time to fit residues: 20.7692 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 : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 71 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10220 Z= 0.257 Angle : 0.580 10.342 13938 Z= 0.290 Chirality : 0.042 0.285 1671 Planarity : 0.004 0.045 1746 Dihedral : 8.199 108.969 1891 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: 0.01 (0.24), residues: 1227 helix: -1.31 (0.48), residues: 89 sheet: 0.45 (0.22), residues: 567 loop : -0.10 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 513 HIS 0.010 0.001 HIS R 41 PHE 0.011 0.001 PHE H 151 TYR 0.017 0.002 TYR R 120 ARG 0.005 0.001 ARG X 331 *********************** 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 : 1.595 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: 0.6226 time to fit residues: 20.0154 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 : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10220 Z= 0.193 Angle : 0.551 10.867 13938 Z= 0.275 Chirality : 0.042 0.356 1671 Planarity : 0.004 0.046 1746 Dihedral : 7.956 108.042 1891 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.24), residues: 1227 helix: -1.08 (0.50), residues: 88 sheet: 0.46 (0.21), residues: 571 loop : 0.06 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP X 513 HIS 0.018 0.001 HIS H 181 PHE 0.013 0.001 PHE H 151 TYR 0.026 0.001 TYR R 120 ARG 0.004 0.000 ARG R 106 *********************** 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 : 1.655 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 revert: symmetry clash REVERT: R 95 GLU cc_start: 0.6082 (tp30) cc_final: 0.5847 (tp30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.7070 time to fit residues: 22.3786 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 : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 40.0000 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** ** H 515 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10220 Z= 0.245 Angle : 0.576 9.552 13938 Z= 0.287 Chirality : 0.042 0.343 1671 Planarity : 0.004 0.046 1746 Dihedral : 7.852 108.263 1891 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % 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: -0.05 (0.24), residues: 1227 helix: -0.98 (0.50), residues: 93 sheet: 0.33 (0.21), residues: 567 loop : -0.11 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP X 513 HIS 0.009 0.002 HIS R 41 PHE 0.010 0.001 PHE X 501 TYR 0.027 0.002 TYR R 120 ARG 0.006 0.001 ARG H 331 *********************** 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 22 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 1.678 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: 0.6855 time to fit residues: 21.4815 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 : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10220 Z= 0.247 Angle : 0.576 9.825 13938 Z= 0.289 Chirality : 0.042 0.332 1671 Planarity : 0.004 0.048 1746 Dihedral : 7.815 108.997 1891 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -0.13 (0.24), residues: 1227 helix: -0.97 (0.50), residues: 93 sheet: 0.24 (0.21), residues: 565 loop : -0.13 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 513 HIS 0.009 0.002 HIS H 181 PHE 0.011 0.001 PHE X 501 TYR 0.031 0.002 TYR R 120 ARG 0.004 0.000 ARG H 331 ********************** 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 : 1.628 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: 0.7099 time to fit residues: 22.1737 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 : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.054910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.039406 restraints weight = 312690.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.041238 restraints weight = 123170.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.042250 restraints weight = 67009.654| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10220 Z= 0.200 Angle : 0.547 9.315 13938 Z= 0.273 Chirality : 0.041 0.281 1671 Planarity : 0.004 0.049 1746 Dihedral : 7.607 107.683 1891 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.24), residues: 1227 helix: -0.91 (0.51), residues: 94 sheet: 0.19 (0.21), residues: 584 loop : 0.05 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 513 HIS 0.006 0.001 HIS H 181 PHE 0.011 0.001 PHE X 501 TYR 0.022 0.001 TYR R 120 ARG 0.003 0.000 ARG R 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.95 seconds wall clock time: 70 minutes 22.38 seconds (4222.38 seconds total)